tool test #1

mvdbeek · 2020-12-09T10:24:53Z

No description provided.

mvdbeek · 2020-12-09T10:26:01Z

/run-tool-test tool_id= addName

mvdbeek · 2020-12-09T10:28:18Z

/run-tool-test tool_id= addName

mvdbeek · 2020-12-09T10:29:25Z

/run-tool-test tool_id= addName

mvdbeek · 2020-12-09T10:32:39Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:12:19Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:25:11Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:30:59Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:33:37Z

Test Results (powered by Planemo) ## Test Summary

| Test State | Count | | ---------- | ----- | | Total | 2 | | Passed | 2 | | Error | 0 | | Failure | 0 | | Skipped | 0 |
Passed Tests
planemo report.md test_result.json tool_test_output.html
✅ addName (Test #1)
Command Line: planemo report.md test_result.json tool_test_output.html `console` Exit Code: planemo report.md test_result.json tool_test_output.html `console 0` Job Parameters: planemo report.md test_result.json tool_test_output.html | Job parameter | Parameter value | | ------------- | --------------- | | header | `{"__current_case__": 0, "colname": "sample", "contains_header": "yes"}` | | prepend | `"false"` | | chromInfo | `"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"` | | dbkey | `"?"` | | __input_ext | `"input"` | planemo report.md test_result.json tool_test_output.html
✅ addName (Test #2)
Command Line: planemo report.md test_result.json tool_test_output.html `console` Exit Code: planemo report.md test_result.json tool_test_output.html `console 0` Job Parameters: planemo report.md test_result.json tool_test_output.html | Job parameter | Parameter value | | ------------- | --------------- | | header | `{"__current_case__": 1, "contains_header": "no"}` | | prepend | `"true"` | | chromInfo | `"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"` | | dbkey | `"?"` | | __input_ext | `"input"` |

mvdbeek · 2020-12-09T11:48:07Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:56:23Z

/run-tool-test tool_id=addName

mvdbeek · 2020-12-09T11:58:16Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	2
Error	0
Failure	0
Skipped	0

Passed Tests

✅ addName (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
header	`{"__current_case__": 0, "colname": "sample", "contains_header": "yes"}`
prepend	`"false"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ addName (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
header	`{"__current_case__": 1, "contains_header": "no"}`
prepend	`"true"`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

mvdbeek · 2020-12-09T12:00:30Z

/run-tool-test tool_id=minimap2

mvdbeek · 2020-12-09T12:06:29Z

/run-tool-test tool_id=minimap2

mvdbeek · 2020-12-09T12:09:13Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	9
Passed	9
Error	0
Failure	0
Skipped	0

Passed Tests

✅ minimap2 (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.066*0.07] collected minimizers
[M::mm_idx_gen::0.067*0.13] sorted minimizers
[M::main::0.067*0.13] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.067*0.13] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.067*0.14] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967
[M::worker_pipeline::0.072*0.23] mapped 100 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x sr -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597955.dat
[M::main] Real time: 0.073 sec; CPU: 0.018 sec; Peak RSS: 0.003 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814782, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "sr", "fastq_input1": {"values": [{"id": 62814787, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "BAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.139*0.04] collected minimizers
[M::mm_idx_gen::0.141*0.06] sorted minimizers
[M::main::0.141*0.06] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.141*0.06] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.141*0.07] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967
[M::worker_pipeline::0.185*0.09] mapped 100 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x sr -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597955.dat
[M::main] Real time: 0.187 sec; CPU: 0.019 sec; Peak RSS: 0.003 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814782, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "sr", "fastq_input1": {"values": [{"id": 62814787, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "CRAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test Test Prokka 1.14.6+galaxy1 #3)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.085*0.06] collected minimizers
[M::mm_idx_gen::0.088*0.11] sorted minimizers
[M::main::0.088*0.11] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.088*0.11] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.088*0.12] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967
[M::worker_pipeline::0.144*0.26] mapped 200 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x sr -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597954.dat /galaxy-repl/main/files/048/597/dataset_48597959.dat
[M::main] Real time: 0.145 sec; CPU: 0.039 sec; Peak RSS: 0.003 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814782, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 1, "analysis_type_selector": "sr", "fastq_input1": {"values": [{"id": 62814786, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 62814791, "src": "hda"}]}, "fastq_input_selector": "paired"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "BAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test Test roary 3.13.0+galaxy2 #4)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.108*0.04] collected minimizers
[M::mm_idx_gen::0.110*0.08] sorted minimizers
[M::main::0.110*0.08] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.110*0.08] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.110*0.08] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967
[M::worker_pipeline::0.185*0.18] mapped 200 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x sr -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597956.dat /galaxy-repl/main/files/048/597/dataset_48597959.dat
[M::main] Real time: 0.186 sec; CPU: 0.034 sec; Peak RSS: 0.003 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814782, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 1, "analysis_type_selector": "sr", "fastq_input1": {"values": [{"id": 62814788, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 62814791, "src": "hda"}]}, "fastq_input_selector": "paired"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "BAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.063*0.07] collected minimizers
[M::mm_idx_gen::0.064*0.14] sorted minimizers
[M::main::0.064*0.15] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.064*0.15] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.064*0.15] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967
[M::worker_pipeline::0.119*0.35] mapped 200 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x sr -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597954.dat /galaxy-repl/main/files/048/597/dataset_48597959.dat
[M::main] Real time: 0.120 sec; CPU: 0.042 sec; Peak RSS: 0.003 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814782, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 2, "analysis_type_selector": "sr", "fastq_input1": {"values": [{"id": 822220, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "BAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.023*0.79] collected minimizers
[M::mm_idx_gen::0.032*1.99] sorted minimizers
[M::main::0.032*1.98] loaded/built the index for 25 target sequence(s)
[M::mm_mapopt_update::0.034*1.93] mid_occ = 3
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 25
[M::mm_idx_stat::0.035*1.90] distinct minimizers: 80111 (99.87% are singletons); average occurrences: 1.002; average spacing: 2.935
[M::worker_pipeline::0.042*2.20] mapped 25 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -x ava-ont -t 6 reference.fa /galaxy-repl/main/files/048/597/dataset_48597951.dat
[M::main] Real time: 0.046 sec; CPU: 0.097 sec; Peak RSS: 0.010 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814783, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "ava-ont", "fastq_input1": {"values": [{"id": 62814783, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "paf"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ minimap2 (Test Test gffread 2.2.1.3+galaxy0 #9)

Command Line:

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.050*0.10] collected minimizers
[M::mm_idx_gen::0.051*0.19] sorted minimizers
[M::main::0.051*0.19] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.051*0.20] mid_occ = 9
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.051*0.20] distinct minimizers: 2920 (98.42% are singletons); average occurrences: 1.022; average spacing: 10.057
[M::worker_pipeline::0.103*0.60] mapped 1 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 -t 6 -a reference.fa /galaxy-repl/main/files/048/597/dataset_48597948.dat
[M::main] Real time: 0.104 sec; CPU: 0.063 sec; Peak RSS: 0.009 GB

Job Parameters:

Job parameter	Parameter value
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 62814779, "src": "hda"}]}, "reference_source_selector": "history"}`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 62814779, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": "false", "I": "", "k": "", "w": ""}`
mapping_options	`{"F": "", "N": "", "X": "false", "f": "", "g": "", "m": "", "max_chain_iter": "", "max_chain_skip": "", "min_occ_floor": "", "n": "", "p": "", "r": ""}`
alignment_options	`{"A": "", "B": "", "E": "", "E2": "", "O": "", "O2": "", "no_end_flt": "true", "s": "", "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "", "z2": ""}`
io_options	`{"K": "", "L": "false", "Q": "false", "Y": "false", "c": "false", "cs": null, "eqx": "false", "output_format": "BAM"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

mvdbeek · 2020-12-09T12:13:27Z

/run-tool-test tool_id=unicycler

mvdbeek · 2021-03-10T15:33:21Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4

mvdbeek · 2021-03-10T16:12:22Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	5
Passed	5
Error	0
Failure	0
Skipped	0

Passed Tests

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

Command Line:

Exit Code:

```
0
```

Standard Output:

INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 03/10/2021 09:49:30 *****
INFO:	Configuring BUSCO with /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0f680480858d2f5838e57feebce6473a9e8f1903a83fbd0c2d1ec3561b77db2d/share/busco/config.ini
INFO:	Mode is genome
WARNING:	You are using a custom e-value cutoff
INFO:	Input file is /galaxy-repl/main/files/052/752/dataset_52752424.dat
INFO:	Downloading information on latest versions of BUSCO data...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
INFO:	Decompressing file '/galaxy-repl/main/jobdir/033/874/33874569/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
INFO:	Running 1 job(s) on makeblastdb, starting at 03/10/2021 09:49:53
INFO:	Creating BLAST database with input file
INFO:	[makeblastdb]	1 of 1 task(s) completed
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 09:49:53
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using fly as species:
INFO:	Running 4 job(s) on augustus, starting at 03/10/2021 09:49:56
INFO:	[augustus]	1 of 4 task(s) completed
INFO:	[augustus]	2 of 4 task(s) completed
INFO:	[augustus]	3 of 4 task(s) completed
INFO:	[augustus]	4 of 4 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 4 job(s) on hmmsearch, starting at 03/10/2021 09:50:14
INFO:	[hmmsearch]	1 of 4 task(s) completed
INFO:	[hmmsearch]	2 of 4 task(s) completed
INFO:	[hmmsearch]	3 of 4 task(s) completed
INFO:	[hmmsearch]	4 of 4 task(s) completed
INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 09:50:17
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Converting predicted genes to short genbank files
INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 03/10/2021 09:50:46
INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
INFO:	Running 1 job(s) on new_species.pl, starting at 03/10/2021 09:50:46
INFO:	[new_species.pl]	1 of 1 task(s) completed
INFO:	Running 1 job(s) on etraining, starting at 03/10/2021 09:50:47
INFO:	[etraining]	1 of 1 task(s) completed
INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
INFO:	Running 32 job(s) on augustus, starting at 03/10/2021 09:50:47
INFO:	[augustus]	4 of 32 task(s) completed
INFO:	[augustus]	7 of 32 task(s) completed
INFO:	[augustus]	10 of 32 task(s) completed
INFO:	[augustus]	13 of 32 task(s) completed
INFO:	[augustus]	17 of 32 task(s) completed
INFO:	[augustus]	20 of 32 task(s) completed
INFO:	[augustus]	23 of 32 task(s) completed
INFO:	[augustus]	26 of 32 task(s) completed
INFO:	[augustus]	29 of 32 task(s) completed
INFO:	[augustus]	32 of 32 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 32 job(s) on hmmsearch, starting at 03/10/2021 09:51:26
INFO:	[hmmsearch]	4 of 32 task(s) completed
INFO:	[hmmsearch]	7 of 32 task(s) completed
INFO:	[hmmsearch]	10 of 32 task(s) completed
INFO:	[hmmsearch]	13 of 32 task(s) completed
INFO:	[hmmsearch]	17 of 32 task(s) completed
INFO:	[hmmsearch]	17 of 32 task(s) completed
INFO:	[hmmsearch]	20 of 32 task(s) completed
INFO:	[hmmsearch]	23 of 32 task(s) completed
INFO:	[hmmsearch]	26 of 32 task(s) completed
INFO:	[hmmsearch]	32 of 32 task(s) completed
INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013      |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1012	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 118 seconds

***** Summary of warnings: *****
WARNING:busco.BuscoConfig	You are using a custom e-value cutoff

INFO:	Results written in /galaxy-repl/main/jobdir/033/874/33874569/working/busco_galaxy

Job Parameters:

Job parameter	Parameter value
mode	`"geno"`
lineage_dataset	`"arthropoda_odb10"`
adv	`{"aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "evalue": "0.01", "limit": "3", "long": "false"}`
__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/busco/busco (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Output:

INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 03/10/2021 10:09:55 *****
INFO:	Configuring BUSCO with /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0f680480858d2f5838e57feebce6473a9e8f1903a83fbd0c2d1ec3561b77db2d/share/busco/config.ini
INFO:	Mode is proteins
WARNING:	You are using a custom e-value cutoff
INFO:	Input file is /galaxy-repl/main/files/052/752/dataset_52752426.dat
INFO:	Downloading information on latest versions of BUSCO data...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
INFO:	Decompressing file '/galaxy-repl/main/jobdir/033/874/33874573/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 1013 job(s) on hmmsearch, starting at 03/10/2021 10:10:14
INFO:	[hmmsearch]	102 of 1013 task(s) completed
INFO:	[hmmsearch]	102 of 1013 task(s) completed
INFO:	[hmmsearch]	102 of 1013 task(s) completed
INFO:	[hmmsearch]	203 of 1013 task(s) completed
INFO:	[hmmsearch]	304 of 1013 task(s) completed
INFO:	[hmmsearch]	304 of 1013 task(s) completed
INFO:	[hmmsearch]	406 of 1013 task(s) completed
INFO:	[hmmsearch]	912 of 1013 task(s) completed
INFO:	[hmmsearch]	912 of 1013 task(s) completed
INFO:	[hmmsearch]	1013 of 1013 task(s) completed
INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013      |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1012	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 54 seconds

***** Summary of warnings: *****
WARNING:busco.BuscoConfig	You are using a custom e-value cutoff

INFO:	Results written in /galaxy-repl/main/jobdir/033/874/33874573/working/busco_galaxy

Job Parameters:

Job parameter	Parameter value
mode	`"prot"`
lineage_dataset	`"arthropoda_odb10"`
adv	`{"aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "evalue": "0.01", "limit": "3", "long": "false"}`
__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/busco/busco (Test Test Prokka 1.14.6+galaxy1 #3)

Command Line:

Exit Code:

```
0
```

Standard Output:

INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 03/10/2021 09:50:22 *****
INFO:	Configuring BUSCO with /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0f680480858d2f5838e57feebce6473a9e8f1903a83fbd0c2d1ec3561b77db2d/share/busco/config.ini
INFO:	Mode is transcriptome
WARNING:	You are using a custom e-value cutoff
INFO:	Input file is /galaxy-repl/main/files/052/752/dataset_52752421.dat
INFO:	Downloading information on latest versions of BUSCO data...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
INFO:	Decompressing file '/galaxy-repl/main/jobdir/033/874/33874570/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
INFO:	Running 1 job(s) on makeblastdb, starting at 03/10/2021 09:50:42
INFO:	Creating BLAST database with input file
INFO:	[makeblastdb]	1 of 1 task(s) completed
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 09:50:42
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Translating candidate transcripts
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 44 job(s) on hmmsearch, starting at 03/10/2021 09:50:59
INFO:	[hmmsearch]	5 of 44 task(s) completed
INFO:	[hmmsearch]	14 of 44 task(s) completed
INFO:	[hmmsearch]	18 of 44 task(s) completed
INFO:	[hmmsearch]	23 of 44 task(s) completed
INFO:	[hmmsearch]	23 of 44 task(s) completed
INFO:	[hmmsearch]	27 of 44 task(s) completed
INFO:	[hmmsearch]	31 of 44 task(s) completed
INFO:	[hmmsearch]	36 of 44 task(s) completed
INFO:	[hmmsearch]	40 of 44 task(s) completed
INFO:	[hmmsearch]	40 of 44 task(s) completed
INFO:	[hmmsearch]	44 of 44 task(s) completed
INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013      |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1012	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 39 seconds

***** Summary of warnings: *****
WARNING:busco.BuscoConfig	You are using a custom e-value cutoff

INFO:	Results written in /galaxy-repl/main/jobdir/033/874/33874570/working/busco_galaxy

Job Parameters:

Job parameter	Parameter value
mode	`"tran"`
lineage_dataset	`"arthropoda_odb10"`
adv	`{"aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "evalue": "0.01", "limit": "3", "long": "false"}`
__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/busco/busco (Test Test roary 3.13.0+galaxy2 #4)

Command Line:

Exit Code:

```
0
```

Standard Output:

INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 03/10/2021 09:51:10 *****
INFO:	Configuring BUSCO with /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0f680480858d2f5838e57feebce6473a9e8f1903a83fbd0c2d1ec3561b77db2d/share/busco/config.ini
INFO:	Mode is genome
WARNING:	You are using a custom e-value cutoff
INFO:	Input file is /galaxy-repl/main/files/052/752/dataset_52752424.dat
INFO:	Downloading information on latest versions of BUSCO data...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
INFO:	Decompressing file '/galaxy-repl/main/jobdir/033/874/33874567/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
WARNING:	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored
INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
INFO:	Running 1 job(s) on makeblastdb, starting at 03/10/2021 09:51:29
INFO:	Creating BLAST database with input file
INFO:	[makeblastdb]	1 of 1 task(s) completed
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 09:51:29
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using human as species:
INFO:	Running 4 job(s) on augustus, starting at 03/10/2021 09:51:31
INFO:	[augustus]	1 of 4 task(s) completed
INFO:	[augustus]	2 of 4 task(s) completed
INFO:	[augustus]	3 of 4 task(s) completed
INFO:	[augustus]	4 of 4 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 4 job(s) on hmmsearch, starting at 03/10/2021 09:51:39
INFO:	[hmmsearch]	1 of 4 task(s) completed
INFO:	[hmmsearch]	2 of 4 task(s) completed
INFO:	[hmmsearch]	3 of 4 task(s) completed
INFO:	[hmmsearch]	4 of 4 task(s) completed
INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 09:51:41
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Converting predicted genes to short genbank files
INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 03/10/2021 09:52:01
INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
INFO:	Running 1 job(s) on new_species.pl, starting at 03/10/2021 09:52:01
INFO:	[new_species.pl]	1 of 1 task(s) completed
INFO:	Running 1 job(s) on etraining, starting at 03/10/2021 09:52:01
INFO:	[etraining]	1 of 1 task(s) completed
INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
INFO:	Running 32 job(s) on augustus, starting at 03/10/2021 09:52:01
INFO:	[augustus]	4 of 32 task(s) completed
INFO:	[augustus]	7 of 32 task(s) completed
INFO:	[augustus]	10 of 32 task(s) completed
INFO:	[augustus]	13 of 32 task(s) completed
INFO:	[augustus]	17 of 32 task(s) completed
INFO:	[augustus]	20 of 32 task(s) completed
INFO:	[augustus]	23 of 32 task(s) completed
INFO:	[augustus]	26 of 32 task(s) completed
INFO:	[augustus]	29 of 32 task(s) completed
INFO:	[augustus]	32 of 32 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 32 job(s) on hmmsearch, starting at 03/10/2021 09:52:28
INFO:	[hmmsearch]	4 of 32 task(s) completed
INFO:	[hmmsearch]	7 of 32 task(s) completed
INFO:	[hmmsearch]	10 of 32 task(s) completed
INFO:	[hmmsearch]	13 of 32 task(s) completed
INFO:	[hmmsearch]	17 of 32 task(s) completed
INFO:	[hmmsearch]	20 of 32 task(s) completed
INFO:	[hmmsearch]	23 of 32 task(s) completed
INFO:	[hmmsearch]	26 of 32 task(s) completed
INFO:	[hmmsearch]	29 of 32 task(s) completed
INFO:	[hmmsearch]	32 of 32 task(s) completed
INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013      |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1012	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 80 seconds

***** Summary of warnings: *****
WARNING:busco.BuscoConfig	You are using a custom e-value cutoff
WARNING:busco.BuscoConfig	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored

INFO:	Results written in /galaxy-repl/main/jobdir/033/874/33874567/working/busco_galaxy

Job Parameters:

Job parameter	Parameter value
mode	`"geno"`
lineage_dataset	`"arthropoda_odb10"`
adv	`{"aug_prediction": {"__current_case__": 2, "augustus_mode": "builtin", "augustus_species": "human"}, "evalue": "0.01", "limit": "3", "long": "false"}`
__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/busco/busco (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

Command Line:

Exit Code:

```
0
```

Standard Output:

INFO:	***** Start a BUSCO v4.1.4 analysis, current time: 03/10/2021 10:10:14 *****
INFO:	Configuring BUSCO with /cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-0f680480858d2f5838e57feebce6473a9e8f1903a83fbd0c2d1ec3561b77db2d/share/busco/config.ini
INFO:	Mode is genome
WARNING:	You are using a custom e-value cutoff
INFO:	Input file is /galaxy-repl/main/files/052/752/dataset_52752424.dat
INFO:	Downloading information on latest versions of BUSCO data...
INFO:	Downloading file 'https://busco-data.ezlab.org/v4/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
INFO:	Decompressing file '/galaxy-repl/main/jobdir/033/874/33874574/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
WARNING:	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored
INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
INFO:	Running 1 job(s) on makeblastdb, starting at 03/10/2021 10:10:39
INFO:	Creating BLAST database with input file
INFO:	[makeblastdb]	1 of 1 task(s) completed
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 10:10:39
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using local as species:
INFO:	Running 4 job(s) on augustus, starting at 03/10/2021 10:10:41
INFO:	[augustus]	1 of 4 task(s) completed
INFO:	[augustus]	2 of 4 task(s) completed
INFO:	[augustus]	3 of 4 task(s) completed
INFO:	[augustus]	4 of 4 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 4 job(s) on hmmsearch, starting at 03/10/2021 10:11:03
INFO:	[hmmsearch]	1 of 4 task(s) completed
INFO:	[hmmsearch]	2 of 4 task(s) completed
INFO:	[hmmsearch]	3 of 4 task(s) completed
INFO:	[hmmsearch]	4 of 4 task(s) completed
INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
INFO:	Running a BLAST search for BUSCOs against created database
INFO:	Running 1 job(s) on tblastn, starting at 03/10/2021 10:11:05
INFO:	[tblastn]	1 of 1 task(s) completed
INFO:	Converting predicted genes to short genbank files
INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 03/10/2021 10:11:29
INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
INFO:	Running 1 job(s) on new_species.pl, starting at 03/10/2021 10:11:29
INFO:	[new_species.pl]	1 of 1 task(s) completed
INFO:	Running 1 job(s) on etraining, starting at 03/10/2021 10:11:30
INFO:	[etraining]	1 of 1 task(s) completed
INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
INFO:	Running Augustus gene predictor on BLAST search results.
INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
INFO:	Running 32 job(s) on augustus, starting at 03/10/2021 10:11:30
INFO:	[augustus]	4 of 32 task(s) completed
INFO:	[augustus]	7 of 32 task(s) completed
INFO:	[augustus]	10 of 32 task(s) completed
INFO:	[augustus]	13 of 32 task(s) completed
INFO:	[augustus]	17 of 32 task(s) completed
INFO:	[augustus]	20 of 32 task(s) completed
INFO:	[augustus]	23 of 32 task(s) completed
INFO:	[augustus]	26 of 32 task(s) completed
INFO:	[augustus]	29 of 32 task(s) completed
INFO:	[augustus]	32 of 32 task(s) completed
INFO:	Extracting predicted proteins...
INFO:	***** Run HMMER on gene sequences *****
INFO:	Running 32 job(s) on hmmsearch, starting at 03/10/2021 10:12:03
INFO:	[hmmsearch]	4 of 32 task(s) completed
INFO:	[hmmsearch]	7 of 32 task(s) completed
INFO:	[hmmsearch]	10 of 32 task(s) completed
INFO:	[hmmsearch]	17 of 32 task(s) completed
INFO:	[hmmsearch]	17 of 32 task(s) completed
INFO:	[hmmsearch]	20 of 32 task(s) completed
INFO:	[hmmsearch]	26 of 32 task(s) completed
INFO:	[hmmsearch]	29 of 32 task(s) completed
INFO:	[hmmsearch]	29 of 32 task(s) completed
INFO:	[hmmsearch]	32 of 32 task(s) completed
INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013      |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1012	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
INFO:	BUSCO analysis done with WARNING(s). Total running time: 110 seconds

***** Summary of warnings: *****
WARNING:busco.BuscoConfig	You are using a custom e-value cutoff
WARNING:busco.BuscoConfig	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored

INFO:	Results written in /galaxy-repl/main/jobdir/033/874/33874574/working/busco_galaxy

Job Parameters:

Job parameter	Parameter value
mode	`"geno"`
lineage_dataset	`"arthropoda_odb10"`
adv	`{"aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 67170593, "src": "hda"}]}}, "evalue": "0.01", "limit": "3", "long": "false"}`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

natefoo · 2021-12-02T20:59:01Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align/0.1.9

mvdbeek · 2021-12-02T21:01:16Z

Results (powered by Planemo)

Summary

State	Count
Total	2
Passed	0
Error	0
Failure	2
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align (Test tool test #1)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align (Test test against test.galaxyproject.org #2)
Problems:
- 'command_line'

natefoo · 2021-12-02T21:53:30Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align/0.1.9

Had to map it to Singularity in the job router conf. Now that tool installs are happening without Conda deps I need to reverse the config - default to Singularity but explicitly exclude (map to non-Singularity dests) all tools that I haven't yet tested.

mvdbeek · 2021-12-02T21:55:31Z

Results (powered by Planemo)

Summary

State	Count
Total	2
Passed	0
Error	0
Failure	2
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align (Test tool test #1)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/wolma/mimodd_aln/mimodd_align (Test test against test.galaxyproject.org #2)
Problems:
- 'command_line'

natefoo · 2021-12-02T21:58:21Z

Well that's odd, it works when I test with galaxy-tool-test from the command line.

natefoo · 2021-12-02T22:03:45Z

As far as the DB is concerned, the tool succeeded both times (the job states are ok), so unless this was an issue with validating the output, not sure what is going on here.

mvdbeek mentioned this issue May 6, 2021

test against test.galaxyproject.org #2

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Test Prokka 1.14.6+galaxy1 #3

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Test roary 3.13.0+galaxy2 #4

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natefoo mentioned this issue Dec 2, 2021

Install wolma/mimodd_aln on .org galaxyproject/usegalaxy-tools#446

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Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

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test mixcr_analyze 3.0.5.0 #67

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test cutadapt 4.0+galaxy1 #68

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test annotatemyids 3.14.0+galaxy1 #69

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test qualimap_bamqc 2.2.2d+galaxy3 + 2.2.2c #70

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test bedtools_genomecoveragebed 2.30.0 #71

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test bg_sortmerna 2.1b.6 #75

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test egsea 1.20.0 #76

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test salmon 1.9.0+galaxy2 #77

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test prokka 1.14.6+galaxy1 #78

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test mothur_unique_seqs 1.39.5.0 #79

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test poretools_winner 0.6.1a1.0 #80

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test tradis_essentiality/1.4.5+galaxy2 #82

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test dropletutils/1.10.0+galaxy2 #88

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test sklearn_searchcv/1.0.8.4 #92

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test bio3d_dccm 2.3.4 #96

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test dada2_mergePairs 1.20+galaxy0 #97

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tool test #1

tool test #1

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tool test #1

tool test #1

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Test Results (powered by Planemo)

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Test Results (powered by Planemo)

Test Summary

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Test Results (powered by Planemo)

Test Summary

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Results (powered by Planemo)

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natefoo commented Dec 2, 2021