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test rnaspades/3.15.4+galaxy2 #87

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jennaj opened this issue Mar 15, 2023 · 7 comments
Closed

test rnaspades/3.15.4+galaxy2 #87

jennaj opened this issue Mar 15, 2023 · 7 comments

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@jennaj
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jennaj commented Mar 15, 2023

toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.15.4+galaxy2
@jennaj
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jennaj commented Mar 15, 2023

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.15.4+galaxy2

@mvdbeek
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mvdbeek commented Mar 15, 2023

Results (powered by Planemo)

Summary

State Count
Total 5
Passed 4
Error 0
Failure 1
Skipped 0
Failed s
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test tool test #1)

    Command Line:

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    Exit Code:
    

      

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      0
      

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    Traceback:
    

      

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    Job Parameters:
    

      

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Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 2, "input1": {"values": [{"id": 109372990, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired_interlaced", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

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    Exit Code:
    

      

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      0
      

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    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input1": {"values": [{"id": 109372984, "src": "hda"}]}, "input2": {"values": [{"id": 109372988, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"33"

      

      
ss
"fr"

      

      
mode_sel
None

      

      
optional_output
["hft", "l", "sft", "tr", "tp"]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Command Line:
    

      

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    Exit Code:
    

      

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      0
      

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    Traceback:
    

      

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      • 

    

    Job Parameters:
    

      

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Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input1": {"values": [{"id": 109372983, "src": "hda"}]}, "input2": {"values": [{"id": 109372987, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

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    Exit Code:
    

      

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      0
      

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    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 3, "input": {"values": [{"id": 1981487, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

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  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Mar 17, 2023


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.15.4+galaxy2

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    











      

  
    

      
        1 similar comment
      
    

  
    

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Mar 20, 2023


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.15.4+galaxy2

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    














      

  
      



  

  @mvdbeek





  


    

      

  

    

        
    
    

  


      
          
  
      
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            mvdbeek
  

      

      

      commented


        Mar 20, 2023


      
    


  





      


        


  
    

      
          
Results (powered by Planemo)


Summary



  

  

  

  

  

  








State
Count






Total
5




Passed
4




Error
0




Failure
1




Skipped
0






Failed s




Passed s

    

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test tool test #1)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Command line: /usr/local/bin/rnaspades.py	-o	/corral4/main/jobs/049/054/49054347/working/output	-t	6	-m	30	--pe-12	1	/corral4/main/jobs/049/054/49054347/working/reads1/ecoli_1K.fastq.gz.fastq.gz	--pe-or	1	fr	

System information:
  SPAdes version: 3.15.4
  Python version: 3.8.12
  OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.10

Output dir: /corral4/main/jobs/049/054/49054347/working/output
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: not specified
      right reads: not specified
      interlaced reads: ['/corral4/main/jobs/049/054/49054347/working/reads1/ecoli_1K.fastq.gz.fastq.gz']
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /corral4/main/jobs/049/054/49054347/working/output/tmp
  Threads: 6
  Memory limit (in Gb): 30


======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/049/054/49054347/working/output/spades.log

/corral4/main/jobs/049/054/49054347/working/reads1/ecoli_1K.fastq.gz.fastq.gz: max reads length: 100

Reads length: 100

K values to be used: [33, 49]

===== Before start started. 


===== Preprocess reads started. 


===== Preprocess reads finished. 


===== Assembling started. 


===== K33 started. 


== Running: /usr/local/bin/spades-core /corral4/main/jobs/049/054/49054347/working/output/K33/configs/config.info /corral4/main/jobs/049/054/49054347/working/output/K33/configs/mda_mode.info /corral4/main/jobs/049/054/49054347/working/output/K33/configs/rna_mode.info

  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054347/working/output/K33/configs/config.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054347/working/output/K33/configs/mda_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054347/working/output/K33/configs/rna_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (memory_limit.cpp          :  54)   Memory limit set to 30 Gb
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 107)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 108)   Maximum k-mer length: 128
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 109)   Assembling dataset (/corral4/main/jobs/049/054/49054347/working/output/dataset.info) with K=33
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 110)   Maximum # of threads to use (adjusted due to OMP capabilities): 6
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 231)   Two-step repeat resolution disabled
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 672)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 673)   Vertex size: 48, edge size: 40
  0:00:00.007     1M / 22M   INFO    General                 (edge_index.hpp            : 113)   Size of edge index entries: 12/8
  0:00:00.007     1M / 22M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.010     1M / 22M   INFO    General                 (read_converter.cpp        :  72)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.010     1M / 22M   INFO    General                 (read_converter.cpp        :  73)   Converting paired reads
  0:00:00.051    43M / 43M   INFO    General                 (binary_converter.cpp      : 111)   2054 reads written
  0:00:00.051    21M / 22M   INFO    General                 (read_converter.cpp        :  86)   Converting single reads
  0:00:00.061    31M / 31M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.062    21M / 22M   INFO    General                 (read_converter.cpp        :  92)   Converting merged reads
  0:00:00.068    31M / 31M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.081     1M / 22M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.106     1M / 22M   INFO    General                 (construction.cpp          : 153)   Max read length 100
  0:00:00.106     1M / 22M   INFO    General                 (construction.cpp          : 159)   Average read length 86.1611
  0:00:00.106     1M / 22M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.106     1M / 22M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:00.110     1M / 22M   INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:00.110     1M / 22M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:00.110     1M / 22M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:00.720     1M / 744M  INFO    General                 (kmer_splitters.hpp        : 131)   Used 8216 reads
  0:00:00.722     1M / 744M  INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:01.108     1M / 744M  INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 974 kmers in total.
  0:00:01.108     1M / 744M  INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:01.213     1M / 744M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 438)   Building kmer index
  0:00:01.213     1M / 744M  INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:01.220     1M / 744M  INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:01.220     1M / 744M  INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:01.220     1M / 744M  INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:01.834  3601M / 3601M INFO    General                 (kmer_splitters.hpp        : 199)   Used 974 kmers.
  0:00:01.834     1M / 746M  INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:02.168     1M / 746M  INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 975 kmers in total.
  0:00:02.168     1M / 746M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:02.196     1M / 746M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 975 kmers, 48240 bytes occupied (395.815 bits per kmer).
  0:00:02.196     1M / 746M  INFO    General                 (kmer_index_builder.hpp    : 169)   Merging final buckets.
  0:00:02.377     1M / 746M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 100)   Building k-mer extensions from k+1-mers
  0:00:02.389     1M / 746M  INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 105)   Building k-mer extensions from k+1-mers finished.
  0:00:02.390     1M / 746M  INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early A/T remover (id: construction:early_at_remover)
  0:00:02.390     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 176)   Remove short poly A/T edges
  0:00:02.391     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 254)   Links removed: 0
  0:00:02.391     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 179)   0 34-mers were removed by early poly A/T remover
  0:00:02.391     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 262)   Remove poly A/T tips
  0:00:02.392     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 331)   Clipped tips: 0
  0:00:02.392     1M / 746M  INFO   Early A/T remover        (early_simplification.hpp  : 265)   0 34-mers were removed by early poly A/T tip clipper
  0:00:02.392     1M / 746M  INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:02.392     1M / 746M  INFO    General                 (construction.cpp          : 301)   Early tip clipper length bound set as (RL - K)
  0:00:02.392     1M / 746M  INFO   Early tip clipping       (early_simplification.hpp  :  47)   Early tip clipping
  0:00:02.393     1M / 746M  INFO   Early tip clipping       (early_simplification.hpp  :  82)   #tipped junctions: 2
  0:00:02.393     1M / 746M  INFO   Early tip clipping       (early_simplification.hpp  :  93)   Clipped tips: 2
  0:00:02.393     1M / 746M  INFO   Early tip clipping       (early_simplification.hpp  :  49)   7 34-mers were removed by early tip clipper
  0:00:02.393     1M / 746M  INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:02.394     1M / 746M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 354)   Extracting unbranching paths
  0:00:02.395     1M / 746M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 373)   Extracting unbranching paths finished. 1 sequences extracted
  0:00:02.395     1M / 746M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 309)   Collecting perfect loops
  0:00:02.396     1M / 746M  INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 342)   Collecting perfect loops finished. 0 loops collected
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 487)   Total 2 edges to create
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 489)   Collecting link records
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 491)   Ordering link records
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 493)   Sorting done
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 503)   Total 2 vertices to create
  0:00:02.396     1M / 746M  INFO    General                 (debruijn_graph_constructor: 506)   Connecting the graph
  0:00:02.396     1M / 746M  INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:02.396     1M / 746M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:02.415     1M / 746M  INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 974 kmers, 48216 bytes occupied (396.025 bits per kmer).
  0:00:02.416     1M / 746M  INFO    General                 (coverage_hash_map_builder.:  47)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:02.424     1M / 746M  INFO    General                 (construction.cpp          : 430)   Filling coverage and flanking coverage from PHM
  0:00:02.491     1M / 746M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == EC Threshold Finding (id: ec_threshold_finder)
  0:00:02.491     1M / 746M  INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 119)   Bucket size: 72
  0:00:02.492     1M / 746M  INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 134)   Proper threshold was not found. Threshold set to 0.1 of average coverage
  0:00:02.492     1M / 746M  INFO    General                 (genomic_info_filler.cpp   :  39)   Average edge coverage: 225.865
  0:00:02.492     1M / 746M  INFO    General                 (genomic_info_filler.cpp   :  40)   Graph threshold: 22.5865
  0:00:02.492     1M / 746M  INFO    General                 (genomic_info_filler.cpp   :  70)   EC coverage threshold value was calculated as 22.5865
  0:00:02.492     1M / 746M  INFO    General                 (genomic_info_filler.cpp   :  71)   Trusted kmer low bound: 0
  0:00:02.492     1M / 746M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:02.492     1M / 746M  INFO    General                 (simplification.cpp        : 106)   PROCEDURE == Initial cleaning
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T short edge remover
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T short edge remover triggered 0 times
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T tip clipper
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T tip clipper triggered 0 times
  0:00:02.492     1M / 746M  INFO    General                 (graph_simplification.hpp  : 703)   Removing loops and rc loops with erroneous connections
  0:00:02.492     1M / 746M  INFO   ECLoopRemover            (erroneous_connection_remov: 406)   Loops: accurately removed/deadend removed/other: 0/0/0
  0:00:02.492     1M / 746M  INFO   ECLoopRemover            (erroneous_connection_remov: 407)   RC loops: accurately removed/deadend removed/other: 0/0/0
  0:00:02.492     1M / 746M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Simplification (id: simplification)
  0:00:02.492     1M / 746M  INFO    General                 (simplification.cpp        : 368)   Graph simplification started
  0:00:02.492     1M / 746M  INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:02.492     1M / 746M  INFO   ConditionParser          (graph_simplification.hpp  : 179)   Creating relative coverage EC condition with threshold 1
  0:00:02.492     1M / 746M  INFO    General                 (simplification.cpp        : 373)   PROCEDURE == Simplification cycle, iteration 1
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running Tip clipper
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 170)   Tip clipper triggered 0 times
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running Dead end clipper
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 170)   Dead end clipper triggered 0 times
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running Bulge remover
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 170)   Bulge remover triggered 0 times
  0:00:02.492     1M / 746M  INFO   Simplification           (parallel_processing.hpp   : 167)   Running Low coverage edge remover
  0:00:02.492     1M / 746M  INFO   ConditionParser          (graph_simplification.hpp  : 179)   Creating relative coverage EC condition with threshold 1
  0:00:02.492     1M / 746M  INFO   Simplific
..
utput)
  0:00:03.135     1M / 744M  INFO    General                 (contig_output.hpp         :  16)   Outputting contigs to /corral4/main/jobs/049/054/49054347/working/output/K49/before_rr.fasta
  0:00:03.145     1M / 744M  INFO    General                 (contig_output_stage.cpp   : 151)   Writing GFA graph to /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph_after_simplification.gfa
  0:00:03.145     1M / 744M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:03.145     1M / 744M  INFO    General                 (graph_pack.cpp            :  77)   Normalizing k-mer map. Total 0 kmers to process
  0:00:03.145     1M / 744M  INFO    General                 (graph_pack.cpp            :  79)   Normalizing done
  0:00:03.145     1M / 744M  INFO    General                 (pair_info_count.cpp       : 339)   Min edge length for estimation: 951
  0:00:03.145     1M / 744M  INFO    General                 (pair_info_count.cpp       : 350)   Estimating insert size for library #0
  0:00:03.145     1M / 744M  INFO    General                 (pair_info_count.cpp       : 202)   Estimating insert size (takes a while)
  0:00:03.196   113M / 744M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.373   113M / 744M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.539   113M / 744M  INFO    General                 (pair_info_count.cpp       : 220)   Edge pairs: 4
  0:00:03.539   113M / 744M  INFO    General                 (pair_info_count.cpp       : 222)   644 paired reads (31.3535% of all) aligned to long edges
  0:00:03.539     1M / 744M  INFO    General                 (pair_info_count.cpp       : 369)     Insert size = 341.047, deviation = 220.565, left quantile = 72, right quantile = 658, read length = 100
  0:00:03.539     1M / 744M  INFO    General                 (pair_info_count.cpp       : 402)   Mapping library #0
  0:00:03.539     1M / 744M  INFO    General                 (pair_info_count.cpp       : 404)   Mapping paired reads (takes a while)
  0:00:03.539     1M / 744M  INFO    General                 (pair_info_count.cpp       : 299)   Left insert size quantile 72, right insert size quantile 658, filtering threshold 0, rounding threshold 0
  0:00:03.548    10M / 744M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.554    10M / 744M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.558     1M / 744M  INFO    General                 (pair_info_count.cpp       : 411)   Mapping single reads of library #0
  0:00:03.558     1M / 744M  INFO    General                 (pair_info_count.cpp       : 266)   Will calculate lib coverage as well
  0:00:03.558     1M / 744M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.580     1M / 744M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 4108 reads processed
  0:00:03.580     1M / 744M  INFO    General                 (pair_info_count.cpp       : 413)   Total paths obtained from single reads: 0
  0:00:03.580     1M / 744M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   : 179)   Processing library #0
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   : 150)   Weight Filter Done
  0:00:03.580     1M / 744M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   :  37)   Filtering info
  0:00:03.580     1M / 744M  INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; library index size: 2
  0:00:03.580     1M / 744M  INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering; library index size: 2
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   : 156)   Refining clustered pair information
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   : 158)   The refining of clustered pair information has been finished
  0:00:03.580     1M / 744M  INFO    General                 (distance_estimation.cpp   : 160)   Improving paired information
  0:00:03.580     1M / 744M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.580     1M / 744M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.580     1M / 744M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:03.580     1M / 744M  INFO    General                 (repeat_resolving.cpp      :  87)   Using Path-Extend repeat resolving
  0:00:03.580     1M / 744M  INFO    General                 (launcher.cpp              : 600)   ExSPAnder repeat resolving tool started
  0:00:03.582     1M / 744M  INFO    General                 (launcher.cpp              : 418)   Creating main extenders, unique edge length = 2000
  0:00:03.582     1M / 744M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.582     1M / 744M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.582     1M / 744M  INFO    General                 (extenders_logic.cpp       : 543)   Using 1 paired-end library
  0:00:03.582     1M / 744M  INFO    General                 (extenders_logic.cpp       : 544)   Using 1 paired-end scaffolding library
  0:00:03.582     1M / 744M  INFO    General                 (extenders_logic.cpp       : 545)   Using 0 single read libraries
  0:00:03.582     1M / 744M  INFO    General                 (launcher.cpp              : 447)   Total number of extenders is 5
  0:00:03.582     1M / 744M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.582     1M / 744M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 454)   Closing gaps in paths
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 484)   Gap closing completed
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 302)   Traversing tandem repeats
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 312)   Traversed 0 loops
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - hard
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.583     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - soft
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.05 converted to 56
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 85 bp converted to 56
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 56
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.2 converted to 71
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 100 bp converted to 71
  0:00:03.585     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 71
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 507)   Finalizing main paths
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.3 converted to 81
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 110 bp converted to 81
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 81
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.6 converted to 111
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 140 bp converted to 111
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 111
  0:00:03.587     1M / 744M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.588     1M / 744M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.588     1M / 744M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.588     1M / 744M  INFO    General                 (launcher.cpp              : 664)   ExSPAnder repeat resolving tool finished
  0:00:03.588     1M / 744M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Contig Output (id: contig_output)
  0:00:03.588     1M / 744M  INFO    General                 (contig_output.hpp         :  16)   Outputting contigs to /corral4/main/jobs/049/054/49054347/working/output/K49/before_rr.fasta
  0:00:03.592     1M / 744M  INFO    General                 (contig_output_stage.cpp   : 151)   Writing GFA graph to /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph_with_scaffolds.gfa
  0:00:03.592     1M / 744M  INFO    General                 (contig_output_stage.cpp   : 165)   Outputting FastG graph to /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph.fastg
  0:00:03.596     1M / 744M  INFO    General                 (contig_output_stage.cpp   :  98)   Outputting contigs to /corral4/main/jobs/049/054/49054347/working/output/K49/transcripts.fasta
  0:00:03.601     1M / 744M  INFO    General                 (contig_output_stage.cpp   : 104)   Outputting FastG paths to /corral4/main/jobs/049/054/49054347/working/output/K49/transcripts.paths
  0:00:03.605     1M / 744M  INFO    General                 (contig_output_stage.cpp   : 111)   Populating GFA with scaffold paths
  0:00:03.608     1M / 744M  INFO    General                 (pipeline.cpp              : 287)   SPAdes finished
  0:00:03.608     1M / 744M  INFO    General                 (main.cpp                  : 136)   Assembling time: 0 hours 0 minutes 3 seconds

===== K49 finished. 


===== Copy files started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /corral4/main/jobs/049/054/49054347/working/output/K49/before_rr.fasta /corral4/main/jobs/049/054/49054347/working/output/before_rr.fasta /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054347/working/output/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054347/working/output/K49/transcripts.fasta /corral4/main/jobs/049/054/49054347/working/output/transcripts.fasta /corral4/main/jobs/049/054/49054347/working/output/K49/transcripts.paths /corral4/main/jobs/049/054/49054347/working/output/transcripts.paths /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054347/working/output/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054347/working/output/K49/assembly_graph.fastg /corral4/main/jobs/049/054/49054347/working/output/assembly_graph.fastg /corral4/main/jobs/049/054/49054347/working/output/K49/hard_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054347/working/output/hard_filtered_transcripts.fasta /corral4/main/jobs/049/054/49054347/working/output/K49/soft_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054347/working/output/soft_filtered_transcripts.fasta


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /corral4/main/jobs/049/054/49054347/working/output/scaffolds.fasta --misc_dir /corral4/main/jobs/049/054/49054347/working/output/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled transcripts are in /corral4/main/jobs/049/054/49054347/working/output/transcripts.fasta
 * Paths in the assembly graph corresponding to the transcripts are in /corral4/main/jobs/049/054/49054347/working/output/transcripts.paths
 * Hard filtered transcripts are in /corral4/main/jobs/049/054/49054347/working/output/hard_filtered_transcripts.fasta
 * Soft filtered transcripts are in /corral4/main/jobs/049/054/49054347/working/output/soft_filtered_transcripts.fasta
 * Assembly graph is in /corral4/main/jobs/049/054/49054347/working/output/assembly_graph.fastg
 * Assembly graph in GFA format is in /corral4/main/jobs/049/054/49054347/working/output/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /corral4/main/jobs/049/054/49054347/working/output/spades.log

Thank you for using SPAdes!

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 2, "input1": {"values": [{"id": 109562255, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired_interlaced", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test test against test.galaxyproject.org #2)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Command line: /usr/local/bin/rnaspades.py	-o	/corral4/main/jobs/049/054/49054370/working/output	-t	6	-m	30	--pe-1	1	/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_1.fastq.gz.fastq.gz	--pe-2	1	/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_2.fastq.gz.fastq.gz	--pe-or	1	fr	--phred-offset	33	--ss	fr	

System information:
  SPAdes version: 3.15.4
  Python version: 3.8.12
  OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.10

Output dir: /corral4/main/jobs/049/054/49054370/working/output
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_1.fastq.gz.fastq.gz']
      right reads: ['/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_2.fastq.gz.fastq.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /corral4/main/jobs/049/054/49054370/working/output/tmp
  Threads: 6
  Memory limit (in Gb): 30


======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/049/054/49054370/working/output/spades.log

/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_1.fastq.gz.fastq.gz: max reads length: 100
/corral4/main/jobs/049/054/49054370/working/paired_reads1/ecoli_1K_2.fastq.gz.fastq.gz: max reads length: 100

Reads length: 100

K values to be used: [33, 49]

===== Before start started. 


===== Assembling started. 


===== K33 started. 


== Running: /usr/local/bin/spades-core /corral4/main/jobs/049/054/49054370/working/output/K33/configs/config.info /corral4/main/jobs/049/054/49054370/working/output/K33/configs/mda_mode.info /corral4/main/jobs/049/054/49054370/working/output/K33/configs/rna_mode.info

  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054370/working/output/K33/configs/config.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054370/working/output/K33/configs/mda_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054370/working/output/K33/configs/rna_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (memory_limit.cpp          :  54)   Memory limit set to 30 Gb
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 107)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 108)   Maximum k-mer length: 128
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 109)   Assembling dataset (/corral4/main/jobs/049/054/49054370/working/output/dataset.info) with K=33
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 110)   Maximum # of threads to use (adjusted due to OMP capabilities): 6
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 231)   Two-step repeat resolution disabled
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 672)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 673)   Vertex size: 48, edge size: 40
  0:00:00.007     1M / 22M   INFO    General                 (edge_index.hpp            : 113)   Size of edge index entries: 12/8
  0:00:00.007     1M / 22M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.016     1M / 22M   INFO    General                 (read_converter.cpp        :  72)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.016     1M / 22M   INFO    General                 (read_converter.cpp        :  73)   Converting paired reads
  0:00:00.065    63M / 63M   INFO    General                 (binary_converter.cpp      : 111)   2054 reads written
  0:00:00.065    41M / 41M   INFO    General                 (read_converter.cpp        :  86)   Converting single reads
  0:00:00.075    51M / 51M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.075    41M / 41M   INFO    General                 (read_converter.cpp        :  92)   Converting merged reads
  0:00:00.078    51M / 51M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.082     1M / 24M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.091     1M / 24M   INFO    General                 (construction.cpp          : 153)   Max read length 100
  0:00:00.091     1M / 24M   INFO    General                 (construction.cpp          : 159)   Average read length 86.1611
  0:00:00.091     1M / 24M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.091     1M / 24M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:00.097     1M / 24M   INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:00.097     1M / 24M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:00.097     1M / 24M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:00.432     1M / 34M   INFO    General                 (kmer_splitters.hpp        : 131)   Used 8216 reads
  0:00:00.433     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:00.918     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 974 kmers in total.
  0:00:00.918     1M / 34M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:01.005     1M / 34M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 438)   Building kmer index
  0:00:01.005     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:01.008     1M / 34M   INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:01.008     1M / 34M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:01.008     1M / 34M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:01.394  3601M / 3601M INFO    General                 (kmer_splitters.hpp        : 199)   Used 974 kmers.
  0:00:01.395     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:01.783     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 975 kmers in total.
  0:00:01.783     1M / 34M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:01.803     1M / 34M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 975 kmers, 48240 bytes occupied (395.815 bits per kmer).
  0:00:01.803     1M / 34M   INFO    General                 (kmer_index_builder.hpp    : 169)   Merging final buckets.
  0:00:01.946     1M / 34M   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 100)   Building k-mer extensions from k+1-mers
  0:00:01.950     1M / 34M   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 105)   Building k-mer extensions from k+1-mers finished.
  0:00:01.950     1M / 34M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early A/T remover (id: construction:early_at_remover)
  0:00:01.950     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 176)   Remove short poly A/T edges
  0:00:01.951     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 254)   Links removed: 0
  0:00:01.951     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 179)   0 34-mers were removed by early poly A/T remover
  0:00:01.951     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 262)   Remove poly A/T tips
  0:00:01.952     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 331)   Clipped tips: 0
  0:00:01.952     1M / 34M   INFO   Early A/T remover        (early_simplification.hpp  : 265)   0 34-mers were removed by early poly A/T tip clipper
  0:00:01.952     1M / 34M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:01.952     1M / 34M   INFO    General                 (construction.cpp          : 301)   Early tip clipper length bound set as (RL - K)
  0:00:01.952     1M / 34M   INFO   Early tip clipping       (early_simplification.hpp  :  47)   Early tip clipping
  0:00:01.952     1M / 34M   INFO   Early tip clipping       (early_simplification.hpp  :  82)   #tipped junctions: 2
  0:00:01.952     1M / 34M   INFO   Early tip clipping       (early_simplification.hpp  :  93)   Clipped tips: 2
  0:00:01.952     1M / 34M   INFO   Early tip clipping       (early_simplification.hpp  :  49)   7 34-mers were removed by early tip clipper
  0:00:01.952     1M / 34M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:01.952     1M / 34M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 354)   Extracting unbranching paths
  0:00:01.953     1M / 34M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 373)   Extracting unbranching paths finished. 1 sequences extracted
  0:00:01.953     1M / 34M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 309)   Collecting perfect loops
  0:00:01.953     1M / 34M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 342)   Collecting perfect loops finished. 0 loops collected
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 487)   Total 2 edges to create
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 489)   Collecting link records
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 491)   Ordering link records
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 493)   Sorting done
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 503)   Total 2 vertices to create
  0:00:01.953     1M / 34M   INFO    General                 (debruijn_graph_constructor: 506)   Connecting the graph
  0:00:01.954     1M / 34M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:01.954     1M / 34M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:01.972     1M / 34M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 974 kmers, 48216 bytes occupied (396.025 bits per kmer).
  0:00:01.973     1M / 34M   INFO    General                 (coverage_hash_map_builder.:  47)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:01.981     1M / 34M   INFO    General                 (construction.cpp          : 430)   Filling coverage and flanking coverage from PHM
  0:00:02.095     1M / 34M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == EC Threshold Finding (id: ec_threshold_finder)
  0:00:02.096     1M / 34M   INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 119)   Bucket size: 72
  0:00:02.096     1M / 34M   INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 134)   Proper threshold was not found. Threshold set to 0.1 of average coverage
  0:00:02.096     1M / 34M   INFO    General                 (genomic_info_filler.cpp   :  39)   Average edge coverage: 225.865
  0:00:02.096     1M / 34M   INFO    General                 (genomic_info_filler.cpp   :  40)   Graph threshold: 22.5865
  0:00:02.096     1M / 34M   INFO    General                 (genomic_info_filler.cpp   :  70)   EC coverage threshold value was calculated as 22.5865
  0:00:02.096     1M / 34M   INFO    General                 (genomic_info_filler.cpp   :  71)   Trusted kmer low bound: 0
  0:00:02.096     1M / 34M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:02.096     1M / 34M   INFO    General                 (simplification.cpp        : 106)   PROCEDURE == Initial cleaning
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T short edge remover
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T short edge remover triggered 0 times
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T tip clipper
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T tip clipper triggered 0 times
  0:00:02.096     1M / 34M   INFO    General                 (graph_simplification.hpp  : 703)   Removing loops and rc loops with erroneous connections
  0:00:02.096     1M / 34M   INFO   ECLoopRemover            (erroneous_connection_remov: 406)   Loops: accurately removed/deadend removed/other: 0/0/0
  0:00:02.096     1M / 34M   INFO   ECLoopRemover            (erroneous_connection_remov: 407)   RC loops: accurately removed/deadend removed/other: 0/0/0
  0:00:02.096     1M / 34M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Simplification (id: simplification)
  0:00:02.096     1M / 34M   INFO    General                 (simplification.cpp        : 368)   Graph simplification started
  0:00:02.096     1M / 34M   INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:02.096     1M / 34M   INFO   ConditionParser          (graph_simplification.hpp  : 179)   Creating relative coverage EC condition with threshold 1
  0:00:02.096     1M / 34M   INFO    General                 (simplification.cpp        : 373)   PROCEDURE == Simplification cycle, iteration 1
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Tip clipper
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 170)   Tip clipper triggered 0 times
  0:00:02.096     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Dead end clipper
  0:00:02.097     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 170)   Dead end clipper triggered 0 times
  0:00:02.097     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Bulge remover
  0:00:02.097     1M / 34M   INFO   Simplification           (parallel_processing.hpp   : 170)   Bulge remover triggered 0 times
  0:00:02.097     1M / 34M   INFO   Simplification           (para
..
ex Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.489     1M / 35M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 951 kmers, 1456 bytes occupied (12.2482 bits per kmer).
  0:00:03.489     1M / 35M   INFO    General                 (edge_index_builders.hpp   : 252)   Collecting edge information from graph, this takes a while.
  0:00:03.489     1M / 35M   INFO    General                 (graph_pack.cpp            :  77)   Normalizing k-mer map. Total 0 kmers to process
  0:00:03.489     1M / 35M   INFO    General                 (graph_pack.cpp            :  79)   Normalizing done
  0:00:03.489     1M / 35M   INFO    General                 (pair_info_count.cpp       : 339)   Min edge length for estimation: 951
  0:00:03.489     1M / 35M   INFO    General                 (pair_info_count.cpp       : 350)   Estimating insert size for library #0
  0:00:03.489     1M / 35M   INFO    General                 (pair_info_count.cpp       : 202)   Estimating insert size (takes a while)
  0:00:03.559   113M / 125M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.732   113M / 125M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.897   113M / 126M  INFO    General                 (pair_info_count.cpp       : 220)   Edge pairs: 2
  0:00:03.897   113M / 126M  INFO    General                 (pair_info_count.cpp       : 222)   1751 paired reads (85.2483% of all) aligned to long edges
  0:00:03.897     1M / 126M  INFO    General                 (pair_info_count.cpp       : 369)     Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100
  0:00:03.897     1M / 126M  INFO    General                 (pair_info_count.cpp       : 402)   Mapping library #0
  0:00:03.897     1M / 126M  INFO    General                 (pair_info_count.cpp       : 404)   Mapping paired reads (takes a while)
  0:00:03.897     1M / 126M  INFO    General                 (pair_info_count.cpp       : 299)   Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0
  0:00:03.926    10M / 126M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.931    10M / 126M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.934     1M / 126M  INFO    General                 (pair_info_count.cpp       : 411)   Mapping single reads of library #0
  0:00:03.934     1M / 126M  INFO    General                 (pair_info_count.cpp       : 266)   Will calculate lib coverage as well
  0:00:03.934     1M / 126M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.947     1M / 126M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 4108 reads processed
  0:00:03.947     1M / 126M  INFO    General                 (pair_info_count.cpp       : 413)   Total paths obtained from single reads: 0
  0:00:03.947     1M / 126M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   : 179)   Processing library #0
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   : 150)   Weight Filter Done
  0:00:03.947     1M / 126M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   :  37)   Filtering info
  0:00:03.947     1M / 126M  INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; library index size: 2
  0:00:03.947     1M / 126M  INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering; library index size: 2
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   : 156)   Refining clustered pair information
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   : 158)   The refining of clustered pair information has been finished
  0:00:03.947     1M / 126M  INFO    General                 (distance_estimation.cpp   : 160)   Improving paired information
  0:00:03.948     1M / 126M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.948     1M / 126M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.948     1M / 126M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:03.948     1M / 126M  INFO    General                 (repeat_resolving.cpp      :  87)   Using Path-Extend repeat resolving
  0:00:03.948     1M / 126M  INFO    General                 (launcher.cpp              : 600)   ExSPAnder repeat resolving tool started
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 418)   Creating main extenders, unique edge length = 2000
  0:00:03.949     1M / 126M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.949     1M / 126M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.949     1M / 126M  INFO    General                 (extenders_logic.cpp       : 543)   Using 1 paired-end library
  0:00:03.949     1M / 126M  INFO    General                 (extenders_logic.cpp       : 544)   Using 1 paired-end scaffolding library
  0:00:03.949     1M / 126M  INFO    General                 (extenders_logic.cpp       : 545)   Using 0 single read libraries
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 447)   Total number of extenders is 5
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 454)   Closing gaps in paths
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 484)   Gap closing completed
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 302)   Traversing tandem repeats
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 312)   Traversed 0 loops
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.949     1M / 126M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 579)   Paths will be printed according to strand-specific coverage
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - hard
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.950     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - soft
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.05 converted to 56
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 85 bp converted to 56
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 56
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.2 converted to 71
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 100 bp converted to 71
  0:00:03.955     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 71
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 507)   Finalizing main paths
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.3 converted to 81
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 110 bp converted to 81
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 81
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.6 converted to 111
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 140 bp converted to 111
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 111
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.958     1M / 126M  INFO    General                 (launcher.cpp              : 664)   ExSPAnder repeat resolving tool finished
  0:00:03.958     1M / 126M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Contig Output (id: contig_output)
  0:00:03.958     1M / 126M  INFO    General                 (contig_output.hpp         :  16)   Outputting contigs to /corral4/main/jobs/049/054/49054370/working/output/K49/before_rr.fasta
  0:00:03.967     1M / 126M  INFO    General                 (contig_output_stage.cpp   : 151)   Writing GFA graph to /corral4/main/jobs/049/054/49054370/working/output/K49/assembly_graph_with_scaffolds.gfa
  0:00:03.967     1M / 126M  INFO    General                 (contig_output_stage.cpp   : 165)   Outputting FastG graph to /corral4/main/jobs/049/054/49054370/working/output/K49/assembly_graph.fastg
  0:00:03.971     1M / 126M  INFO    General                 (contig_output_stage.cpp   :  98)   Outputting contigs to /corral4/main/jobs/049/054/49054370/working/output/K49/transcripts.fasta
  0:00:03.977     1M / 126M  INFO    General                 (contig_output_stage.cpp   : 104)   Outputting FastG paths to /corral4/main/jobs/049/054/49054370/working/output/K49/transcripts.paths
  0:00:03.978     1M / 126M  INFO    General                 (contig_output_stage.cpp   : 111)   Populating GFA with scaffold paths
  0:00:03.984     1M / 126M  INFO    General                 (pipeline.cpp              : 287)   SPAdes finished
  0:00:03.984     1M / 126M  INFO    General                 (main.cpp                  : 136)   Assembling time: 0 hours 0 minutes 3 seconds

===== K49 finished. 


===== Copy files started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /corral4/main/jobs/049/054/49054370/working/output/K49/before_rr.fasta /corral4/main/jobs/049/054/49054370/working/output/before_rr.fasta /corral4/main/jobs/049/054/49054370/working/output/K49/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054370/working/output/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054370/working/output/K49/transcripts.fasta /corral4/main/jobs/049/054/49054370/working/output/transcripts.fasta /corral4/main/jobs/049/054/49054370/working/output/K49/transcripts.paths /corral4/main/jobs/049/054/49054370/working/output/transcripts.paths /corral4/main/jobs/049/054/49054370/working/output/K49/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054370/working/output/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054370/working/output/K49/assembly_graph.fastg /corral4/main/jobs/049/054/49054370/working/output/assembly_graph.fastg /corral4/main/jobs/049/054/49054370/working/output/K49/hard_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054370/working/output/hard_filtered_transcripts.fasta /corral4/main/jobs/049/054/49054370/working/output/K49/soft_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054370/working/output/soft_filtered_transcripts.fasta


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /corral4/main/jobs/049/054/49054370/working/output/scaffolds.fasta --misc_dir /corral4/main/jobs/049/054/49054370/working/output/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled transcripts are in /corral4/main/jobs/049/054/49054370/working/output/transcripts.fasta
 * Paths in the assembly graph corresponding to the transcripts are in /corral4/main/jobs/049/054/49054370/working/output/transcripts.paths
 * Hard filtered transcripts are in /corral4/main/jobs/049/054/49054370/working/output/hard_filtered_transcripts.fasta
 * Soft filtered transcripts are in /corral4/main/jobs/049/054/49054370/working/output/soft_filtered_transcripts.fasta
 * Assembly graph is in /corral4/main/jobs/049/054/49054370/working/output/assembly_graph.fastg
 * Assembly graph in GFA format is in /corral4/main/jobs/049/054/49054370/working/output/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /corral4/main/jobs/049/054/49054370/working/output/spades.log

Thank you for using SPAdes!

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input1": {"values": [{"id": 109562248, "src": "hda"}]}, "input2": {"values": [{"id": 109562254, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"33"

      

      
ss
"fr"

      

      
mode_sel
None

      

      
optional_output
["hft", "l", "sft", "tr", "tp"]

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test Test Prokka 1.14.6+galaxy1 #3)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Output:
    

      

    • 

      Command line: /usr/local/bin/rnaspades.py	-o	/corral4/main/jobs/049/054/49054374/working/output	-t	6	-m	30	--pe-1	1	/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_1.fasta.gz.fasta.gz	--pe-2	1	/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_2.fasta.gz.fasta.gz	--pe-or	1	fr	

System information:
  SPAdes version: 3.15.4
  Python version: 3.8.12
  OS: Linux-4.18.0-372.9.1.el8.x86_64-x86_64-with-glibc2.10

Output dir: /corral4/main/jobs/049/054/49054374/working/output
Debug mode is turned OFF

Dataset parameters:
  RNA-seq mode
  Reads:
    Library number: 1, library type: paired-end
      orientation: fr
      left reads: ['/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_1.fasta.gz.fasta.gz']
      right reads: ['/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_2.fasta.gz.fasta.gz']
      interlaced reads: not specified
      single reads: not specified
      merged reads: not specified
Assembly parameters:
  k: automatic selection based on read length
  Repeat resolution is enabled
  Mismatch careful mode is turned OFF
  MismatchCorrector will be SKIPPED
  Coverage cutoff is turned OFF
Other parameters:
  Dir for temp files: /corral4/main/jobs/049/054/49054374/working/output/tmp
  Threads: 6
  Memory limit (in Gb): 30


======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/049/054/49054374/working/output/spades.log

/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_1.fasta.gz.fasta.gz: max reads length: 100
/corral4/main/jobs/049/054/49054374/working/paired_reads1/ecoli_1K_2.fasta.gz.fasta.gz: max reads length: 100

Reads length: 100

K values to be used: [33, 49]

===== Before start started. 


===== Assembling started. 


===== K33 started. 


== Running: /usr/local/bin/spades-core /corral4/main/jobs/049/054/49054374/working/output/K33/configs/config.info /corral4/main/jobs/049/054/49054374/working/output/K33/configs/mda_mode.info /corral4/main/jobs/049/054/49054374/working/output/K33/configs/rna_mode.info

  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054374/working/output/K33/configs/config.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054374/working/output/K33/configs/mda_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  :  99)   Loaded config from /corral4/main/jobs/049/054/49054374/working/output/K33/configs/rna_mode.info
  0:00:00.000     1M / 22M   INFO    General                 (memory_limit.cpp          :  54)   Memory limit set to 30 Gb
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 107)   Starting SPAdes, built from N/A, git revision N/A
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 108)   Maximum k-mer length: 128
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 109)   Assembling dataset (/corral4/main/jobs/049/054/49054374/working/output/dataset.info) with K=33
  0:00:00.000     1M / 22M   INFO    General                 (main.cpp                  : 110)   Maximum # of threads to use (adjusted due to OMP capabilities): 6
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 212)   SPAdes started
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 225)   Starting from stage: read_conversion
  0:00:00.000     1M / 22M   INFO    General                 (pipeline.cpp              : 231)   Two-step repeat resolution disabled
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 672)   Graph created, vertex min_id: 3, edge min_id: 3
  0:00:00.007     1M / 22M   INFO   GraphCore                (graph_core.hpp            : 673)   Vertex size: 48, edge size: 40
  0:00:00.007     1M / 22M   INFO    General                 (edge_index.hpp            : 113)   Size of edge index entries: 12/8
  0:00:00.007     1M / 22M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Binary Read Conversion (id: read_conversion)
  0:00:00.016     1M / 22M   INFO    General                 (read_converter.cpp        :  72)   Converting reads to binary format for library #0 (takes a while)
  0:00:00.017     1M / 22M   INFO    General                 (read_converter.cpp        :  73)   Converting paired reads
  0:00:00.051    63M / 63M   INFO    General                 (binary_converter.cpp      : 111)   2054 reads written
  0:00:00.052    41M / 41M   INFO    General                 (read_converter.cpp        :  86)   Converting single reads
  0:00:00.060    51M / 51M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.060    41M / 41M   INFO    General                 (read_converter.cpp        :  92)   Converting merged reads
  0:00:00.073    51M / 51M   INFO    General                 (binary_converter.cpp      : 111)   0 reads written
  0:00:00.096     1M / 24M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == de Bruijn graph construction (id: construction)
  0:00:00.159     1M / 24M   INFO    General                 (construction.cpp          : 153)   Max read length 100
  0:00:00.159     1M / 24M   INFO    General                 (construction.cpp          : 159)   Average read length 86.1611
  0:00:00.159     1M / 24M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == k+1-mer counting (id: construction:kpomer_counting)
  0:00:00.159     1M / 24M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:00.166     1M / 24M   INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:00.166     1M / 24M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:00.166     1M / 24M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:01.233     1M / 40M   INFO    General                 (kmer_splitters.hpp        : 131)   Used 8216 reads
  0:00:01.234     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:01.989     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 974 kmers in total.
  0:00:01.989     1M / 40M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Extension index construction (id: construction:extension_index_construction)
  0:00:02.028     1M / 40M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 438)   Building kmer index
  0:00:02.028     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 243)   Splitting kmer instances into 60 files using 6 threads. This might take a while.
  0:00:02.031     1M / 40M   INFO    General                 (file_limit.hpp            :  42)   Open file limit set to 131072
  0:00:02.031     1M / 40M   INFO    General                 (kmer_splitter.hpp         :  93)   Memory available for splitting buffers: 1.66665 Gb
  0:00:02.031     1M / 40M   INFO    General                 (kmer_splitter.hpp         : 101)   Using cell size of 559240
  0:00:02.561  3601M / 3601M INFO    General                 (kmer_splitters.hpp        : 199)   Used 974 kmers.
  0:00:02.561     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 249)   Starting k-mer counting.
  0:00:03.326     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 260)   K-mer counting done. There are 975 kmers in total.
  0:00:03.326     1M / 40M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.353     1M / 40M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 975 kmers, 48240 bytes occupied (395.815 bits per kmer).
  0:00:03.353     1M / 40M   INFO    General                 (kmer_index_builder.hpp    : 169)   Merging final buckets.
  0:00:03.516     1M / 40M   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 100)   Building k-mer extensions from k+1-mers
  0:00:03.522     1M / 40M   INFO   DeBruijnExtensionIndexBu (kmer_extension_index_build: 105)   Building k-mer extensions from k+1-mers finished.
  0:00:03.522     1M / 40M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early A/T remover (id: construction:early_at_remover)
  0:00:03.522     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 176)   Remove short poly A/T edges
  0:00:03.523     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 254)   Links removed: 0
  0:00:03.523     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 179)   0 34-mers were removed by early poly A/T remover
  0:00:03.523     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 262)   Remove poly A/T tips
  0:00:03.523     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 331)   Clipped tips: 0
  0:00:03.523     1M / 40M   INFO   Early A/T remover        (early_simplification.hpp  : 265)   0 34-mers were removed by early poly A/T tip clipper
  0:00:03.523     1M / 40M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Early tip clipping (id: construction:early_tip_clipper)
  0:00:03.523     1M / 40M   INFO    General                 (construction.cpp          : 301)   Early tip clipper length bound set as (RL - K)
  0:00:03.523     1M / 40M   INFO   Early tip clipping       (early_simplification.hpp  :  47)   Early tip clipping
  0:00:03.526     1M / 40M   INFO   Early tip clipping       (early_simplification.hpp  :  82)   #tipped junctions: 2
  0:00:03.526     1M / 40M   INFO   Early tip clipping       (early_simplification.hpp  :  93)   Clipped tips: 2
  0:00:03.526     1M / 40M   INFO   Early tip clipping       (early_simplification.hpp  :  49)   7 34-mers were removed by early tip clipper
  0:00:03.526     1M / 40M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Condensing graph (id: construction:graph_condensing)
  0:00:03.526     1M / 40M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 354)   Extracting unbranching paths
  0:00:03.526     1M / 40M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 373)   Extracting unbranching paths finished. 1 sequences extracted
  0:00:03.527     1M / 40M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 309)   Collecting perfect loops
  0:00:03.527     1M / 40M   INFO   UnbranchingPathExtractor (debruijn_graph_constructor: 342)   Collecting perfect loops finished. 0 loops collected
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 487)   Total 2 edges to create
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 489)   Collecting link records
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 491)   Ordering link records
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 493)   Sorting done
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 503)   Total 2 vertices to create
  0:00:03.527     1M / 40M   INFO    General                 (debruijn_graph_constructor: 506)   Connecting the graph
  0:00:03.527     1M / 40M   INFO    General                 (stage.cpp                 : 117)   PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm)
  0:00:03.527     1M / 40M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 395)   Building perfect hash indices
  0:00:03.541     1M / 40M   INFO   K-mer Index Building     (kmer_index_builder.hpp    : 431)   Index built. Total 974 kmers, 48216 bytes occupied (396.025 bits per kmer).
  0:00:03.541     1M / 40M   INFO    General                 (coverage_hash_map_builder.:  47)   Collecting k-mer coverage information from reads, this takes a while.
  0:00:03.550     1M / 40M   INFO    General                 (construction.cpp          : 430)   Filling coverage and flanking coverage from PHM
  0:00:03.597     1M / 40M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == EC Threshold Finding (id: ec_threshold_finder)
  0:00:03.597     1M / 40M   INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 119)   Bucket size: 72
  0:00:03.597     1M / 40M   INFO   ThresholdFinder          (ec_threshold_finder.hpp   : 134)   Proper threshold was not found. Threshold set to 0.1 of average coverage
  0:00:03.597     1M / 40M   INFO    General                 (genomic_info_filler.cpp   :  39)   Average edge coverage: 225.865
  0:00:03.597     1M / 40M   INFO    General                 (genomic_info_filler.cpp   :  40)   Graph threshold: 22.5865
  0:00:03.597     1M / 40M   INFO    General                 (genomic_info_filler.cpp   :  70)   EC coverage threshold value was calculated as 22.5865
  0:00:03.597     1M / 40M   INFO    General                 (genomic_info_filler.cpp   :  71)   Trusted kmer low bound: 0
  0:00:03.597     1M / 40M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Raw Simplification (id: raw_simplification)
  0:00:03.597     1M / 40M   INFO    General                 (simplification.cpp        : 106)   PROCEDURE == Initial cleaning
  0:00:03.597     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T short edge remover
  0:00:03.597     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T short edge remover triggered 0 times
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running poly A/T tip clipper
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 170)   poly A/T tip clipper triggered 0 times
  0:00:03.598     1M / 40M   INFO    General                 (graph_simplification.hpp  : 703)   Removing loops and rc loops with erroneous connections
  0:00:03.598     1M / 40M   INFO   ECLoopRemover            (erroneous_connection_remov: 406)   Loops: accurately removed/deadend removed/other: 0/0/0
  0:00:03.598     1M / 40M   INFO   ECLoopRemover            (erroneous_connection_remov: 407)   RC loops: accurately removed/deadend removed/other: 0/0/0
  0:00:03.598     1M / 40M   INFO   StageManager             (stage.cpp                 : 185)   STAGE == Simplification (id: simplification)
  0:00:03.598     1M / 40M   INFO    General                 (simplification.cpp        : 368)   Graph simplification started
  0:00:03.598     1M / 40M   INFO    General                 (graph_simplification.hpp  : 634)   Creating parallel br instance
  0:00:03.598     1M / 40M   INFO   ConditionParser          (graph_simplification.hpp  : 179)   Creating relative coverage EC condition with threshold 1
  0:00:03.598     1M / 40M   INFO    General                 (simplification.cpp        : 373)   PROCEDURE == Simplification cycle, iteration 1
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Tip clipper
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 170)   Tip clipper triggered 0 times
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Dead end clipper
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 170)   Dead end clipper triggered 0 times
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 167)   Running Bulge remover
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 170)   Bulge remover triggered 0 times
  0:00:03.598     1M / 40M   INFO   Simplification           (parallel_processing.hpp   : 16
..
ut)
  0:00:02.675     1M / 760M  INFO    General                 (contig_output.hpp         :  16)   Outputting contigs to /corral4/main/jobs/049/054/49054374/working/output/K49/before_rr.fasta
  0:00:02.682     1M / 760M  INFO    General                 (contig_output_stage.cpp   : 151)   Writing GFA graph to /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph_after_simplification.gfa
  0:00:02.684     1M / 760M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Paired Information Counting (id: late_pair_info_count)
  0:00:02.684     1M / 760M  INFO    General                 (graph_pack.cpp            :  77)   Normalizing k-mer map. Total 0 kmers to process
  0:00:02.684     1M / 760M  INFO    General                 (graph_pack.cpp            :  79)   Normalizing done
  0:00:02.684     1M / 760M  INFO    General                 (pair_info_count.cpp       : 339)   Min edge length for estimation: 951
  0:00:02.684     1M / 760M  INFO    General                 (pair_info_count.cpp       : 350)   Estimating insert size for library #0
  0:00:02.684     1M / 760M  INFO    General                 (pair_info_count.cpp       : 202)   Estimating insert size (takes a while)
  0:00:02.737   113M / 760M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:02.913   113M / 760M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.079   113M / 760M  INFO    General                 (pair_info_count.cpp       : 220)   Edge pairs: 2
  0:00:03.079   113M / 760M  INFO    General                 (pair_info_count.cpp       : 222)   1751 paired reads (85.2483% of all) aligned to long edges
  0:00:03.079     1M / 760M  INFO    General                 (pair_info_count.cpp       : 369)     Insert size = 214.709, deviation = 10.4946, left quantile = 201, right quantile = 228, read length = 100
  0:00:03.079     1M / 760M  INFO    General                 (pair_info_count.cpp       : 402)   Mapping library #0
  0:00:03.079     1M / 760M  INFO    General                 (pair_info_count.cpp       : 404)   Mapping paired reads (takes a while)
  0:00:03.079     1M / 760M  INFO    General                 (pair_info_count.cpp       : 299)   Left insert size quantile 201, right insert size quantile 228, filtering threshold 0, rounding threshold 0
  0:00:03.126    10M / 760M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.132    10M / 760M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 2054 reads processed
  0:00:03.136     1M / 760M  INFO    General                 (pair_info_count.cpp       : 411)   Mapping single reads of library #0
  0:00:03.136     1M / 760M  INFO    General                 (pair_info_count.cpp       : 266)   Will calculate lib coverage as well
  0:00:03.136     1M / 760M  INFO    General                 (pair_info_count.cpp       :  48)   Selecting usual mapper
  0:00:03.164     1M / 760M  INFO    General                 (sequence_mapper_notifier.h:  95)   Total 4108 reads processed
  0:00:03.164     1M / 760M  INFO    General                 (pair_info_count.cpp       : 413)   Total paths obtained from single reads: 0
  0:00:03.164     1M / 760M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Distance Estimation (id: distance_estimation)
  0:00:03.164     1M / 760M  INFO    General                 (distance_estimation.cpp   : 179)   Processing library #0
  0:00:03.164     1M / 760M  INFO    General                 (distance_estimation.cpp   : 150)   Weight Filter Done
  0:00:03.164     1M / 760M  INFO   DistanceEstimator        (distance_estimation.hpp   : 116)   Using SIMPLE distance estimator
  0:00:03.165     1M / 760M  INFO    General                 (distance_estimation.cpp   :  37)   Filtering info
  0:00:03.165     1M / 760M  INFO    General                 (pair_info_filters.hpp     : 242)   Start filtering; library index size: 2
  0:00:03.165     1M / 760M  INFO    General                 (pair_info_filters.hpp     : 263)   Done filtering; library index size: 2
  0:00:03.165     1M / 760M  INFO    General                 (distance_estimation.cpp   : 156)   Refining clustered pair information
  0:00:03.165     1M / 760M  INFO    General                 (distance_estimation.cpp   : 158)   The refining of clustered pair information has been finished
  0:00:03.165     1M / 760M  INFO    General                 (distance_estimation.cpp   : 160)   Improving paired information
  0:00:03.165     1M / 760M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.165     1M / 760M  INFO   PairInfoImprover         (pair_info_improver.hpp    : 104)   Paired info stats: missing = 0; contradictional = 0
  0:00:03.165     1M / 760M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Repeat Resolving (id: repeat_resolving)
  0:00:03.165     1M / 760M  INFO    General                 (repeat_resolving.cpp      :  87)   Using Path-Extend repeat resolving
  0:00:03.165     1M / 760M  INFO    General                 (launcher.cpp              : 600)   ExSPAnder repeat resolving tool started
  0:00:03.170     1M / 760M  INFO    General                 (launcher.cpp              : 418)   Creating main extenders, unique edge length = 2000
  0:00:03.171     1M / 760M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.171     1M / 760M  INFO    General                 (extenders_logic.cpp       : 345)   Creating extender; library index size: 2
  0:00:03.171     1M / 760M  INFO    General                 (extenders_logic.cpp       : 543)   Using 1 paired-end library
  0:00:03.171     1M / 760M  INFO    General                 (extenders_logic.cpp       : 544)   Using 1 paired-end scaffolding library
  0:00:03.171     1M / 760M  INFO    General                 (extenders_logic.cpp       : 545)   Using 0 single read libraries
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 447)   Total number of extenders is 5
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 454)   Closing gaps in paths
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 484)   Gap closing completed
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 302)   Traversing tandem repeats
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 312)   Traversed 0 loops
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 250)   Finalizing paths
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 252)   Deduplicating paths
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 256)   Paths deduplicated
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 263)   Overlaps will not be removed
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 273)   Paths finalized
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - hard
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 2 converted to 151
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 180 bp converted to 151
  0:00:03.171     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 151
  0:00:03.175     1M / 760M  INFO    General                 (launcher.cpp              : 499)   Finalizing paths - soft
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.05 converted to 56
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 85 bp converted to 56
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 56
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.2 converted to 71
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 100 bp converted to 71
  0:00:03.176     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 71
  0:00:03.179     1M / 760M  INFO    General                 (launcher.cpp              : 507)   Finalizing main paths
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.3 converted to 81
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 110 bp converted to 81
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 81
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.6 converted to 111
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 140 bp converted to 111
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 111
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 295)   Read length relative cutoff 1.5 converted to 101
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 296)   Read length absolute cutoff 130 bp converted to 101
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 297)   Length cutoff: 101
  0:00:03.180     1M / 760M  INFO    General                 (launcher.cpp              : 664)   ExSPAnder repeat resolving tool finished
  0:00:03.180     1M / 760M  INFO   StageManager             (stage.cpp                 : 185)   STAGE == Contig Output (id: contig_output)
  0:00:03.180     1M / 760M  INFO    General                 (contig_output.hpp         :  16)   Outputting contigs to /corral4/main/jobs/049/054/49054374/working/output/K49/before_rr.fasta
  0:00:03.189     1M / 760M  INFO    General                 (contig_output_stage.cpp   : 151)   Writing GFA graph to /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph_with_scaffolds.gfa
  0:00:03.189     1M / 760M  INFO    General                 (contig_output_stage.cpp   : 165)   Outputting FastG graph to /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph.fastg
  0:00:03.195     1M / 760M  INFO    General                 (contig_output_stage.cpp   :  98)   Outputting contigs to /corral4/main/jobs/049/054/49054374/working/output/K49/transcripts.fasta
  0:00:03.198     1M / 760M  INFO    General                 (contig_output_stage.cpp   : 104)   Outputting FastG paths to /corral4/main/jobs/049/054/49054374/working/output/K49/transcripts.paths
  0:00:03.201     1M / 760M  INFO    General                 (contig_output_stage.cpp   : 111)   Populating GFA with scaffold paths
  0:00:03.207     1M / 760M  INFO    General                 (pipeline.cpp              : 287)   SPAdes finished
  0:00:03.207     1M / 760M  INFO    General                 (main.cpp                  : 136)   Assembling time: 0 hours 0 minutes 3 seconds

===== K49 finished. 


===== Copy files started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /corral4/main/jobs/049/054/49054374/working/output/K49/before_rr.fasta /corral4/main/jobs/049/054/49054374/working/output/before_rr.fasta /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054374/working/output/assembly_graph_after_simplification.gfa /corral4/main/jobs/049/054/49054374/working/output/K49/transcripts.fasta /corral4/main/jobs/049/054/49054374/working/output/transcripts.fasta /corral4/main/jobs/049/054/49054374/working/output/K49/transcripts.paths /corral4/main/jobs/049/054/49054374/working/output/transcripts.paths /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054374/working/output/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/049/054/49054374/working/output/K49/assembly_graph.fastg /corral4/main/jobs/049/054/49054374/working/output/assembly_graph.fastg /corral4/main/jobs/049/054/49054374/working/output/K49/hard_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054374/working/output/hard_filtered_transcripts.fasta /corral4/main/jobs/049/054/49054374/working/output/K49/soft_filtered_final_paths.fasta /corral4/main/jobs/049/054/49054374/working/output/soft_filtered_transcripts.fasta


===== Copy files finished. 


===== Assembling finished. 


===== Breaking scaffolds started. 


== Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /corral4/main/jobs/049/054/49054374/working/output/scaffolds.fasta --misc_dir /corral4/main/jobs/049/054/49054374/working/output/misc --threshold_for_breaking_scaffolds 3


===== Breaking scaffolds finished. 


===== Terminate started. 


===== Terminate finished. 

 * Assembled transcripts are in /corral4/main/jobs/049/054/49054374/working/output/transcripts.fasta
 * Paths in the assembly graph corresponding to the transcripts are in /corral4/main/jobs/049/054/49054374/working/output/transcripts.paths
 * Hard filtered transcripts are in /corral4/main/jobs/049/054/49054374/working/output/hard_filtered_transcripts.fasta
 * Soft filtered transcripts are in /corral4/main/jobs/049/054/49054374/working/output/soft_filtered_transcripts.fasta
 * Assembly graph is in /corral4/main/jobs/049/054/49054374/working/output/assembly_graph.fastg
 * Assembly graph in GFA format is in /corral4/main/jobs/049/054/49054374/working/output/assembly_graph_with_scaffolds.gfa

======= SPAdes pipeline finished.

SPAdes log can be found here: /corral4/main/jobs/049/054/49054374/working/output/spades.log

Thank you for using SPAdes!

      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input1": {"values": [{"id": 109562247, "src": "hda"}]}, "input2": {"values": [{"id": 109562252, "src": "hda"}]}, "orientation": "fr", "sPaired": "paired", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades (Test Test roary 3.13.0+galaxy2 #4)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Traceback:
    

      

    • 

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 3, "input": {"values": [{"id": 1989557, "src": "hdca"}]}, "orientation": "fr", "sPaired": "paired_collection", "type_paired": "pe"}

      

      
additional_reads
{"__current_case__": 1, "selector": "false"}

      

      
arf
{"flrna": null, "nanopore": null, "pacbio": null, "trusted_contigs": null, "untrusted_contigs": null}

      

      
kmer_cond
{"__current_case__": 0, "kmer_sel": "auto"}

      

      
phred_offset
"auto"

      

      
ss
"no"

      

      
mode_sel
None

      

      
optional_output
"tr"

      

      
__job_resource
{"__current_case__": 0, "__job_resource__select": "no"}

      

      
chromInfo
"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 




      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Mar 30, 2023


      
    


  





      


        


  
    

      
          
/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/rnaspades/rnaspades/3.15.4+galaxy2

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @jennaj





  


    

      

  

    

        
    
    

  


      
          
  
      
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            jennaj
  

      

      

      commented


        Jun 12, 2023


      
    


  





      


        


  
    

      
          
Recent bugs included success runs of this tool too

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    

      
    

    


      

          @jennaj
jennaj




            closed this as completed


      Jun 12, 2023

    

  


    











  
  

    

      

  





  




  
  

              

  
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      2 participants
    

    

        
          @mvdbeek 
        
          @jennaj