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Test trim_galore 0.6.7+galaxy0 #10

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jennaj opened this issue Jan 28, 2022 · 4 comments
Closed

Test trim_galore 0.6.7+galaxy0 #10

jennaj opened this issue Jan 28, 2022 · 4 comments

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@jennaj
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jennaj commented Jan 28, 2022

Installed at galaxyproject/usegalaxy-tools#456
@jennaj
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jennaj commented Jan 28, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0

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@natefoo
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natefoo commented Jan 28, 2022

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.7+galaxy0

@mvdbeek
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mvdbeek commented Jan 28, 2022

Results (powered by Planemo)

Summary

State Count
Total 14
Passed 14
Error 0
Failure 0
Skipped 0
Passed s
  • ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test tool test #1)

    Command Line:

    • 

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456897/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
smallRNA	0	TGGAATTCTCGG	2	0.00
Nextera	0	CTGTCTCTTATA	2	0.00
Illumina	0	AGATCGGAAGAGC	2	0.00
Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Nextera: 0, count Illumina: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).

Writing report to '/corral4/main/jobs/040/456/40456897/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.04 s (22008 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

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    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq -> /corral4/main/objects/e/c/d/dataset_ecd1f88d-7b1d-4dd1-a4c7-14d570d951a1.dat
-rw-r--r--    1 g2main   G-803372    1.8K Jan 28 14:38 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     508 Jan 28 14:38 input_1_trimmed.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746738, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 0, "retain_unpaired_select": "no_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456899/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illumina	0	AGATCGGAAGAGC	2	0.00
Nextera	0	CTGTCTCTTATA	2	0.00
smallRNA	0	TGGAATTCTCGG	2	0.00
Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0, count smallRNA: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).

Writing report to '/corral4/main/jobs/040/456/40456899/working/input_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.02 s (10655 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq.gz -> /corral4/main/objects/0/d/0/dataset_0d07fb66-0480-4018-816b-985c0f2c3ceb.dat
-rw-r--r--    1 g2main   G-803372    1.9K Jan 28 14:38 input_1.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     291 Jan 28 14:38 input_1_trimmed.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746740, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 0, "retain_unpaired_select": "no_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test racon 1.3.1.1 #11)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456917/working/
Hard-trimming from 5'-end selected. File(s) will be trimmed to leave the rightmost 20 bp on the 3'-end, and Trim Galore will then exit.

Input file name:  input_1.fastq
Writing trimmed version (using the last 20 bp only) of the input file 'input_1.fastq' to 'input_1.20bp_3prime.fq'

Finished writing out converted version of the FastQ file input_1.fastq (99 sequences in total)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Input file name:  input_2.fastq
Writing trimmed version (using the last 20 bp only) of the input file 'input_2.fastq' to 'input_2.20bp_3prime.fq'

Finished writing out converted version of the FastQ file input_2.fastq (99 sequences in total)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:39 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:39 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_1.fastq -> /corral4/main/objects/6/d/5/dataset_6d501a12-270a-4bc6-acdc-0e0244a37046.dat
-rw-r--r--    1 g2main   G-803372    8.7K Jan 28 14:39 input_1_hardtrim.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_2.fastq -> /corral4/main/objects/e/4/8/dataset_e48ccc66-6b72-49ee-922c-6c142702c08d.dat
-rw-r--r--    1 g2main   G-803372    8.7K Jan 28 14:39 input_2_hardtrim.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746787, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746788, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 1, "clock": "false", "hardtrim3": "20", "hardtrim5": "", "polyA": "false", "settingsType": "custom"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test mafft 7.221.3 #12)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456916/working/
Hard-trimming from the 3'-end selected. File(s) will be trimmed to leave the leftmost 20 bp on the 5'-end, and Trim Galore will then exit.

Input file name:  input_1.fastq
Writing trimmed version (using the first 20 bp only) of the input file 'input_1.fastq' to 'input_1.20bp_5prime.fq'

Finished writing out converted version of the FastQ file input_1.fastq (99 sequences in total)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Input file name:  input_2.fastq
Writing trimmed version (using the first 20 bp only) of the input file 'input_2.fastq' to 'input_2.20bp_5prime.fq'

Finished writing out converted version of the FastQ file input_2.fastq (99 sequences in total)

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:39 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:39 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_1.fastq -> /corral4/main/objects/6/d/5/dataset_6d501a12-270a-4bc6-acdc-0e0244a37046.dat
-rw-r--r--    1 g2main   G-803372    8.7K Jan 28 14:39 input_1_hardtrim.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_2.fastq -> /corral4/main/objects/e/4/8/dataset_e48ccc66-6b72-49ee-922c-6c142702c08d.dat
-rw-r--r--    1 g2main   G-803372    8.7K Jan 28 14:39 input_2_hardtrim.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746787, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746788, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 1, "clock": "false", "hardtrim3": "", "hardtrim5": "20", "polyA": "false", "settingsType": "custom"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456918/working/

IT'S TIME FOR CLOCK PROCESSING!!!									[pun intended]

Writing dual trimmed version of the input file 'input_1.fastq' to 'input_1.clock_UMI.R1.fq'
Writing dual trimmed version of the input file 'input_2.fastq' to 'input_2.clock_UMI.R2.fq'
                 ---
Sequences processed in total: 99
thereof had fixed sequence CAGT in both R1 and R2:	 99 (100.00%)
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~


Pre-processing finished...

Please run Trim Galore again to remove adapters, poor quality bases as well as UMI/fixed sequences from the 3'-end of the reads.
A sample command for this is:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
trim_galore --paired --three_prime_clip_R1 15 --three_prime_clip_R2 15 *.clock_UMI.R1.fq.gz *.clock_UMI.R2.fq.gz
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Trim Galore Epigenetic Clock processing complete.


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:39 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:39 ..
-rw-r--r--    1 g2main   G-803372   54.8K Jan 28 14:39 input_1.clock_UMI.R1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_1.fastq -> /corral4/main/objects/6/d/5/dataset_6d501a12-270a-4bc6-acdc-0e0244a37046.dat
-rw-r--r--    1 g2main   G-803372   54.8K Jan 28 14:39 input_2.clock_UMI.R2.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_2.fastq -> /corral4/main/objects/e/4/8/dataset_e48ccc66-6b72-49ee-922c-6c142702c08d.dat

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746787, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746788, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 1, "clock": "true", "hardtrim3": "", "hardtrim5": "", "polyA": "false", "settingsType": "custom"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test ebi_search_rest_results 0.1.1 #14)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456921/working/


AUTO-DETECTING POLY-A TYPE
===========================
Attempting to auto-detect PolyA type from the first 1 million sequences of the first file (>> input_1.fastq <<)

Found perfect matches for the following mono-polymer sequences:
Poly-nucleotide type	Count	Sequence	Sequences analysed	Percentage
PolyA	3	AAAAAAAAAA	99	3.03
PolyT	0	TTTTTTTTTT	99	0.00
Using PolyA Polymer for trimming (count: 3). Second best hit was PolyT (count: 0)

Writing report to '/corral4/main/jobs/040/456/40456921/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AAAAAAAAAAAAAAAAAAAA' (Poly-A Read 1; auto-detected)
Maximum trimming error rate: 0.1 (default)
Optional adapter 2 sequence (only used for read 2 of paired-end files): 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT'
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq

POLY-A TRIMMING MODE; EXPERIMENTAL!!

  >>> Now performing Poly-A trimming for the adapter sequence: 'AAAAAAAAAAAAAAAAAAAA' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -O 1 -a AAAAAAAAAAAAAAAAAAAA /corral4/main/jobs/040/456/40456921/working/input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.02 s (252 µs/read; 0.24 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        21 (21.2%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):         24,825 bp (99.9%)

=== Adapter 1 ===

Sequence: AAAAAAAAAAAAAAAAAAAA; Type: regular 3'; Length: 20; Trimmed: 21 times

No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20 bp: 2

Bases preceding removed adapters:
  A: 0.0%
  C: 19.0%
  G: 52.4%
  T: 28.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	18	24.8	0	18
2	3	6.2	0	3

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/corral4/main/jobs/040/456/40456921/working/input_2.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AAAAAAAAAAAAAAAAAAAA' (Poly-A Read 1; auto-detected)
Maximum trimming error rate: 0.1 (default)
Optional adapter 2 sequence (only used for read 2 of paired-end files): 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT'
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j -j 1
Writing final adapter and quality trimmed output to input_2_trimmed.fq

POLY-A TRIMMING MODE; EXPERIMENTAL!!

  >>> Now performing Poly-A trimming for the adapter sequence: 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT' from file input_2.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -O 1 -g TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT /corral4/main/jobs/040/456/40456921/working/input_2.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.08 s (808 µs/read; 0.07 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        13 (13.1%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):         24,828 bp (99.9%)

=== Adapter 1 ===

Sequence: TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT; Type: regular 5'; Length: 150; Trimmed: 13 times

No. of allowed errors:
1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-59 bp: 5; 60-69 bp: 6; 70-79 bp: 7; 80-89 bp: 8; 90-99 bp: 9; 100-109 bp: 10; 110-119 bp: 11; 120-129 bp: 12; 130-139 bp: 13; 140-149 bp: 14; 150 bp: 15

Overview of removed sequences
length	count	expect	max.err	error counts
1	5	24.8	0	5
2	8	6.2	0	8

RUN STATISTICS FOR INPUT FILE: input_2.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files input_1_trimmed.fq and input_2_trimmed.fq
file_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq


>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<
Writing validated paired-end Read 1 reads to input_1_val_1.fq
Writing validated paired-end Read 2 reads to input_2_val_2.fq

Total number of sequences analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 0 (0.00%)

Deleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq

====================================================================================================


      

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    Standard Output:
    

      

    • 

      total 5K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:39 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:39 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_1.fastq -> /corral4/main/objects/6/d/5/dataset_6d501a12-270a-4bc6-acdc-0e0244a37046.dat
-rw-r--r--    1 g2main   G-803372    1.7K Jan 28 14:39 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   53.6K Jan 28 14:39 input_1_val_1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:39 input_2.fastq -> /corral4/main/objects/e/4/8/dataset_e48ccc66-6b72-49ee-922c-6c142702c08d.dat
-rw-r--r--    1 g2main   G-803372    2.3K Jan 28 14:39 input_2.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   53.5K Jan 28 14:39 input_2_val_2.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746787, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746788, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 1, "clock": "false", "hardtrim3": "", "hardtrim5": "", "polyA": "true", "settingsType": "custom"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (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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    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456895/working/
Writing report to '/corral4/main/jobs/040/456/40456895/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.02 s (11225 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

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    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq -> /corral4/main/objects/e/c/d/dataset_ecd1f88d-7b1d-4dd1-a4c7-14d570d951a1.dat
-rw-r--r--    1 g2main   G-803372    1.6K Jan 28 14:38 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     508 Jan 28 14:38 input_1_trimmed.fq

      

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    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746738, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 1, "trimming_select": "--illumina"}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

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

    Command Line:
    

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456896/working/
Writing report to '/corral4/main/jobs/040/456/40456896/working/input_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.04 s (18046 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

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    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq.gz -> /corral4/main/objects/0/d/0/dataset_0d07fb66-0480-4018-816b-985c0f2c3ceb.dat
-rw-r--r--    1 g2main   G-803372    1.6K Jan 28 14:38 input_1.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     291 Jan 28 14:38 input_1_trimmed.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746740, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 1, "trimming_select": "--illumina"}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456894/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
smallRNA	0	TGGAATTCTCGG	2	0.00
Nextera	0	CTGTCTCTTATA	2	0.00
Illumina	0	AGATCGGAAGAGC	2	0.00
Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Nextera: 0, count Illumina: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).

Writing report to '/corral4/main/jobs/040/456/40456894/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.01 s (7208 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq -> /corral4/main/objects/e/c/d/dataset_ecd1f88d-7b1d-4dd1-a4c7-14d570d951a1.dat
-rw-r--r--    1 g2main   G-803372    1.8K Jan 28 14:38 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     508 Jan 28 14:38 input_1_trimmed.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746738, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test trinotate 3.2.2+galaxy0 #6)
    

    Command Line:
    

      

    • 

      

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    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456898/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
smallRNA	0	TGGAATTCTCGG	2	0.00
Nextera	0	CTGTCTCTTATA	2	0.00
Illumina	0	AGATCGGAAGAGC	2	0.00
Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Nextera: 0, count Illumina: 0)
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).

Writing report to '/corral4/main/jobs/040/456/40456898/working/input_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: single-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 20 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.02 s (10263 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       2
Reads with adapters:                         1 (50.0%)
Reads written (passing filters):             2 (100.0%)

Total basepairs processed:           188 bp
Quality-trimmed:                      20 bp (10.6%)
Total written (filtered):            167 bp (88.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times

No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1	0.5	0	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
2 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp:	0 (0.0%)


      

      • 

    

    Standard Output:
    

      

    • 

      total 4K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq.gz -> /corral4/main/objects/0/d/0/dataset_0d07fb66-0480-4018-816b-985c0f2c3ceb.dat
-rw-r--r--    1 g2main   G-803372    1.9K Jan 28 14:38 input_1.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     291 Jan 28 14:38 input_1_trimmed.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 0, "input_singles": {"values": [{"id": 92746740, "src": "hda"}]}, "sPaired": "single", "three_prime_clip_R1": "", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 0, "settingsType": "default"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test pangolin 3.1.17+galaxy1 #7)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456901/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Nextera	29	CTGTCTCTTATA	99	29.29
smallRNA	0	TGGAATTCTCGG	99	0.00
Illumina	0	AGATCGGAAGAGC	99	0.00
Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)

Writing report to '/corral4/main/jobs/040/456/40456901/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.03 s (276 µs/read; 0.22 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        52 (52.5%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     205 bp (0.8%)
Total written (filtered):         23,339 bp (93.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 9.6%
  C: 38.5%
  G: 23.1%
  T: 28.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11	24.8	0	11
2	5	6.2	0	5
3	3	1.5	0	3
4	3	0.4	0	3
12	1	0.0	1	1
13	2	0.0	1	2
14	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	0 1
20	2	0.0	1	2
21	1	0.0	1	1
24	1	0.0	1	1
26	2	0.0	1	2
31	1	0.0	1	1
33	1	0.0	1	1
41	2	0.0	1	2
49	1	0.0	1	1
50	1	0.0	1	1
54	1	0.0	1	1
56	1	0.0	1	1
58	2	0.0	1	2
60	1	0.0	1	1
67	2	0.0	1	2
68	1	0.0	1	1
69	1	0.0	1	1
73	1	0.0	1	1
80	1	0.0	1	1
86	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/corral4/main/jobs/040/456/40456901/working/input_2.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j -j 1
Writing final adapter and quality trimmed output to input_2_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.07 s (681 µs/read; 0.09 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        58 (58.6%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     745 bp (3.0%)
Total written (filtered):         23,035 bp (92.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 12.1%
  C: 37.9%
  G: 8.6%
  T: 41.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16	24.8	0	16
2	7	6.2	0	7
3	1	1.5	0	1
4	2	0.4	0	2
6	2	0.0	0	2
9	1	0.0	0	1
10	1	0.0	1	1
13	1	0.0	1	1
14	2	0.0	1	2
15	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	1
19	2	0.0	1	2
21	1	0.0	1	1
25	1	0.0	1	1
30	1	0.0	1	1
32	2	0.0	1	2
34	1	0.0	1	1
36	2	0.0	1	2
38	1	0.0	1	1
40	1	0.0	1	1
41	1	0.0	1	1
42	1	0.0	1	1
43	1	0.0	1	1
49	1	0.0	1	1
51	1	0.0	1	1
56	1	0.0	1	1
57	1	0.0	1	1
60	1	0.0	1	1
67	1	0.0	1	1
80	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_2.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files input_1_trimmed.fq and input_2_trimmed.fq
file_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq


>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<
Writing validated paired-end Read 1 reads to input_1_val_1.fq
Writing validated paired-end Read 2 reads to input_2_val_2.fq

Total number of sequences analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)

Deleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq

====================================================================================================


      

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    Standard Output:
    

      

    • 

      total 5K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq -> /corral4/main/objects/3/6/0/dataset_3604ef05-2139-4df4-94c8-231b08d98692.dat
-rw-r--r--    1 g2main   G-803372    1.9K Jan 28 14:38 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   49.9K Jan 28 14:38 input_1_val_1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_2.fastq -> /corral4/main/objects/f/b/7/dataset_fb77193b-2d80-4dcb-bd19-dc510792a6e5.dat
-rw-r--r--    1 g2main   G-803372    2.1K Jan 28 14:38 input_2.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   49.8K Jan 28 14:38 input_2_val_2.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746745, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746749, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 0, "retain_unpaired_select": "no_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

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      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456903/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Nextera	29	CTGTCTCTTATA	99	29.29
Illumina	0	AGATCGGAAGAGC	99	0.00
smallRNA	0	TGGAATTCTCGG	99	0.00
Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)

Writing report to '/corral4/main/jobs/040/456/40456903/working/input_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.02 s (210 µs/read; 0.29 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        52 (52.5%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     205 bp (0.8%)
Total written (filtered):         23,339 bp (93.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 9.6%
  C: 38.5%
  G: 23.1%
  T: 28.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11	24.8	0	11
2	5	6.2	0	5
3	3	1.5	0	3
4	3	0.4	0	3
12	1	0.0	1	1
13	2	0.0	1	2
14	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	0 1
20	2	0.0	1	2
21	1	0.0	1	1
24	1	0.0	1	1
26	2	0.0	1	2
31	1	0.0	1	1
33	1	0.0	1	1
41	2	0.0	1	2
49	1	0.0	1	1
50	1	0.0	1	1
54	1	0.0	1	1
56	1	0.0	1	1
58	2	0.0	1	2
60	1	0.0	1	1
67	2	0.0	1	2
68	1	0.0	1	1
69	1	0.0	1	1
73	1	0.0	1	1
80	1	0.0	1	1
86	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/corral4/main/jobs/040/456/40456903/working/input_2.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j -j 1
Writing final adapter and quality trimmed output to input_2_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.03 s (317 µs/read; 0.19 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        58 (58.6%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     745 bp (3.0%)
Total written (filtered):         23,035 bp (92.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 12.1%
  C: 37.9%
  G: 8.6%
  T: 41.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16	24.8	0	16
2	7	6.2	0	7
3	1	1.5	0	1
4	2	0.4	0	2
6	2	0.0	0	2
9	1	0.0	0	1
10	1	0.0	1	1
13	1	0.0	1	1
14	2	0.0	1	2
15	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	1
19	2	0.0	1	2
21	1	0.0	1	1
25	1	0.0	1	1
30	1	0.0	1	1
32	2	0.0	1	2
34	1	0.0	1	1
36	2	0.0	1	2
38	1	0.0	1	1
40	1	0.0	1	1
41	1	0.0	1	1
42	1	0.0	1	1
43	1	0.0	1	1
49	1	0.0	1	1
51	1	0.0	1	1
56	1	0.0	1	1
57	1	0.0	1	1
60	1	0.0	1	1
67	1	0.0	1	1
80	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz
file_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<
Writing validated paired-end Read 1 reads to input_1_val_1.fq.gz
Writing validated paired-end Read 2 reads to input_2_val_2.fq.gz

Total number of sequences analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)

Deleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz

====================================================================================================


      

      • 

    

    Standard Output:
    

      

    • 

      total 5K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq.gz -> /corral4/main/objects/0/a/7/dataset_0a787972-703c-401b-b8b0-485c69885a9f.dat
-rw-r--r--    1 g2main   G-803372    2.0K Jan 28 14:38 input_1.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   10.7K Jan 28 14:38 input_1_val_1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_2.fastq.gz -> /corral4/main/objects/9/c/f/dataset_9cf10c69-1a4a-48e8-8d8d-802fb7c98f9b.dat
-rw-r--r--    1 g2main   G-803372    2.2K Jan 28 14:38 input_2.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372   10.5K Jan 28 14:38 input_2_val_2.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 1, "input_mate1": {"values": [{"id": 92746743, "src": "hda"}]}, "input_mate2": {"values": [{"id": 92746747, "src": "hda"}]}, "sPaired": "paired", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 0, "retain_unpaired_select": "no_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test gffread 2.2.1.3+galaxy0 #9)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456905/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Nextera	29	CTGTCTCTTATA	99	29.29
smallRNA	0	TGGAATTCTCGG	99	0.00
Illumina	0	AGATCGGAAGAGC	99	0.00
Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)

Writing report to '/corral4/main/jobs/040/456/40456905/working/input_1.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bb (default)

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.03 s (297 µs/read; 0.20 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        52 (52.5%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     205 bp (0.8%)
Total written (filtered):         23,339 bp (93.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 9.6%
  C: 38.5%
  G: 23.1%
  T: 28.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11	24.8	0	11
2	5	6.2	0	5
3	3	1.5	0	3
4	3	0.4	0	3
12	1	0.0	1	1
13	2	0.0	1	2
14	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	0 1
20	2	0.0	1	2
21	1	0.0	1	1
24	1	0.0	1	1
26	2	0.0	1	2
31	1	0.0	1	1
33	1	0.0	1	1
41	2	0.0	1	2
49	1	0.0	1	1
50	1	0.0	1	1
54	1	0.0	1	1
56	1	0.0	1	1
58	2	0.0	1	2
60	1	0.0	1	1
67	2	0.0	1	2
68	1	0.0	1	1
69	1	0.0	1	1
73	1	0.0	1	1
80	1	0.0	1	1
86	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/corral4/main/jobs/040/456/40456905/working/input_2.fastq_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bb (default)

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j -j 1
Writing final adapter and quality trimmed output to input_2_trimmed.fq


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
Processing reads on 1 core in single-end mode ...
Finished in 0.04 s (358 µs/read; 0.17 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        58 (58.6%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     745 bp (3.0%)
Total written (filtered):         23,035 bp (92.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 12.1%
  C: 37.9%
  G: 8.6%
  T: 41.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16	24.8	0	16
2	7	6.2	0	7
3	1	1.5	0	1
4	2	0.4	0	2
6	2	0.0	0	2
9	1	0.0	0	1
10	1	0.0	1	1
13	1	0.0	1	1
14	2	0.0	1	2
15	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	1
19	2	0.0	1	2
21	1	0.0	1	1
25	1	0.0	1	1
30	1	0.0	1	1
32	2	0.0	1	2
34	1	0.0	1	1
36	2	0.0	1	2
38	1	0.0	1	1
40	1	0.0	1	1
41	1	0.0	1	1
42	1	0.0	1	1
43	1	0.0	1	1
49	1	0.0	1	1
51	1	0.0	1	1
56	1	0.0	1	1
57	1	0.0	1	1
60	1	0.0	1	1
67	1	0.0	1	1
80	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_2.fastq
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files input_1_trimmed.fq and input_2_trimmed.fq
file_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq


>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<
Writing validated paired-end Read 1 reads to input_1_val_1.fq
Writing validated paired-end Read 2 reads to input_2_val_2.fq

Writing unpaired read 1 reads to input_1_unpaired_1.fq
Writing unpaired read 2 reads to input_2_unpaired_2.fq

Total number of sequences analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)

Deleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq

====================================================================================================


      

      • 

    

    Standard Output:
    

      

    • 

      total 6K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq -> /corral4/main/objects/3/6/0/dataset_3604ef05-2139-4df4-94c8-231b08d98692.dat
-rw-r--r--    1 g2main   G-803372    2.0K Jan 28 14:38 input_1.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     551 Jan 28 14:38 input_1_unpaired_1.fq
-rw-r--r--    1 g2main   G-803372   49.9K Jan 28 14:38 input_1_val_1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_2.fastq -> /corral4/main/objects/f/b/7/dataset_fb77193b-2d80-4dcb-bd19-dc510792a6e5.dat
-rw-r--r--    1 g2main   G-803372    2.2K Jan 28 14:38 input_2.fastq_trimming_report.txt
-rw-r--r--    1 g2main   G-803372       0 Jan 28 14:38 input_2_unpaired_2.fq
-rw-r--r--    1 g2main   G-803372   49.8K Jan 28 14:38 input_2_val_2.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 2, "input_mate_pairs": {"values": [{"id": 1366454, "src": "hdca"}]}, "sPaired": "paired_collection", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 1, "length_1": "35", "length_2": "35", "retain_unpaired_select": "retain_unpaired_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

    • 

  • 

    ✅ toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore (Test Test trim_galore 0.6.7+galaxy0 #10)
    

    Command Line:
    

      

    • 

      

      • 

    

    Exit Code:
    

      

    • 

      0
      

      • 

    

    Standard Error:
    

      

    • 

      Proceeding with single-core trimming (user-defined)
Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')
Cutadapt version: 3.4
single-core operation.
Output will be written into the directory: /corral4/main/jobs/040/456/40456902/working/


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Nextera	29	CTGTCTCTTATA	99	29.29
Illumina	0	AGATCGGAAGAGC	99	0.00
smallRNA	0	TGGAATTCTCGG	99	0.00
Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)

Writing report to '/corral4/main/jobs/040/456/40456902/working/input_1.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bb (default)
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j 1
Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.04 s (382 µs/read; 0.16 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        52 (52.5%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     205 bp (0.8%)
Total written (filtered):         23,339 bp (93.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 9.6%
  C: 38.5%
  G: 23.1%
  T: 28.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11	24.8	0	11
2	5	6.2	0	5
3	3	1.5	0	3
4	3	0.4	0	3
12	1	0.0	1	1
13	2	0.0	1	2
14	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	0 1
20	2	0.0	1	2
21	1	0.0	1	1
24	1	0.0	1	1
26	2	0.0	1	2
31	1	0.0	1	1
33	1	0.0	1	1
41	2	0.0	1	2
49	1	0.0	1	1
50	1	0.0	1	1
54	1	0.0	1	1
56	1	0.0	1	1
58	2	0.0	1	2
60	1	0.0	1	1
67	2	0.0	1	2
68	1	0.0	1	1
69	1	0.0	1	1
73	1	0.0	1	1
80	1	0.0	1	1
86	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/corral4/main/jobs/040/456/40456902/working/input_2.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: input_2.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.7
Cutadapt version: 3.4
Number of cores used for trimming: 1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bb (default)
Output file(s) will be GZIP compressed

Cutadapt seems to be fairly up-to-date (version 3.4). Setting -j -j 1
Writing final adapter and quality trimmed output to input_2_trimmed.fq.gz


  >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq.gz <<< 
This is cutadapt 3.4 with Python 3.9.6
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz
Processing reads on 1 core in single-end mode ...
Finished in 0.04 s (369 µs/read; 0.16 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                        58 (58.6%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     745 bp (3.0%)
Total written (filtered):         23,035 bp (92.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times

No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 12.1%
  C: 37.9%
  G: 8.6%
  T: 41.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	16	24.8	0	16
2	7	6.2	0	7
3	1	1.5	0	1
4	2	0.4	0	2
6	2	0.0	0	2
9	1	0.0	0	1
10	1	0.0	1	1
13	1	0.0	1	1
14	2	0.0	1	2
15	1	0.0	1	1
16	1	0.0	1	1
17	1	0.0	1	1
19	2	0.0	1	2
21	1	0.0	1	1
25	1	0.0	1	1
30	1	0.0	1	1
32	2	0.0	1	2
34	1	0.0	1	1
36	2	0.0	1	2
38	1	0.0	1	1
40	1	0.0	1	1
41	1	0.0	1	1
42	1	0.0	1	1
43	1	0.0	1	1
49	1	0.0	1	1
51	1	0.0	1	1
56	1	0.0	1	1
57	1	0.0	1	1
60	1	0.0	1	1
67	1	0.0	1	1
80	1	0.0	1	1

RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz
=============================================
99 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz
file_1: input_1_trimmed.fq.gz, file_2: input_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq.gz and input_2_trimmed.fq.gz <<<<<
Writing validated paired-end Read 1 reads to input_1_val_1.fq.gz
Writing validated paired-end Read 2 reads to input_2_val_2.fq.gz

Writing unpaired read 1 reads to input_1_unpaired_1.fq.gz
Writing unpaired read 2 reads to input_2_unpaired_2.fq.gz

Total number of sequences analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)

Deleting both intermediate output files input_1_trimmed.fq.gz and input_2_trimmed.fq.gz

====================================================================================================


      

      • 

    

    Standard Output:
    

      

    • 

      total 6K     
drwxr-xr-x    2 g2main   G-803372    4.0K Jan 28 14:38 .
drwxr-xr-x   12 g2main   G-803372    4.0K Jan 28 14:38 ..
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_1.fastq.gz -> /corral4/main/objects/0/a/7/dataset_0a787972-703c-401b-b8b0-485c69885a9f.dat
-rw-r--r--    1 g2main   G-803372    2.1K Jan 28 14:38 input_1.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372     255 Jan 28 14:38 input_1_unpaired_1.fq
-rw-r--r--    1 g2main   G-803372   10.7K Jan 28 14:38 input_1_val_1.fq
lrwxrwxrwx    1 g2main   G-803372      76 Jan 28 14:38 input_2.fastq.gz -> /corral4/main/objects/9/c/f/dataset_9cf10c69-1a4a-48e8-8d8d-802fb7c98f9b.dat
-rw-r--r--    1 g2main   G-803372    2.3K Jan 28 14:38 input_2.fastq.gz_trimming_report.txt
-rw-r--r--    1 g2main   G-803372      20 Jan 28 14:38 input_2_unpaired_2.fq
-rw-r--r--    1 g2main   G-803372   10.5K Jan 28 14:38 input_2_val_2.fq

      

      • 

    

    Job Parameters:
    

      

    • 

      


      
Job parameter
Parameter value

      
      


      
singlePaired
{"__current_case__": 2, "input_mate_pairs": {"values": [{"id": 1366451, "src": "hdca"}]}, "sPaired": "paired_collection", "three_prime_clip_R1": "", "three_prime_clip_R2": "", "trim1": "false", "trimming": {"__current_case__": 0, "trimming_select": ""}}

      

      
params
{"__current_case__": 1, "clip_R1": "", "clip_R2": "", "error_rate": "0.1", "min_length": "20", "quality": "20", "report": "true", "retain_unpaired": {"__current_case__": 1, "length_1": "35", "length_2": "35", "retain_unpaired_select": "retain_unpaired_output"}, "settingsType": "custom", "stringency": "1"}

      

      
rrbs
{"__current_case__": 0, "settingsType": "default"}

      

      
trimming
{"__current_case__": 0, "settingsType": "default"}

      

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

      

      
dbkey
"?"

      

      
__input_ext
"input"

      
      

      

      • 

    

    

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