test busco 5.4.6+galaxy0 #95

jennaj · 2023-06-07T19:58:31Z

toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

jennaj · 2023-06-07T19:58:52Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

mvdbeek · 2023-06-07T20:06:44Z

Results (powered by Planemo)

Summary

State	Count
Total	8
Passed	1
Error	0
Failure	7
Skipped	0

Failed s

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

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900944/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900944/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900944/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900946/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900946/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900946/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900940/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900940/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900940/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900952/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900952/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900952/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900952/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900952/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900952/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900952/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 2, "augustus_mode": "builtin", "augustus_species": "human"}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900951/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900951/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900951/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900951/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900951/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900951/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900951/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 112948064, "src": "hda"}]}}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/iuc/busco/busco (Test Test trinotate 3.2.2+galaxy0 #6)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900943/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900943/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900943/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/iuc/busco/busco (Test Test pangolin 3.1.17+galaxy1 #7)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0, exit_code: 16, stderr: Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found
.

Command Line:

Exit Code:

```
16
```

Standard Error:

Failed to initialize root file catalog (16 - file catalog failure)

/scratch4/nekrut/galaxy/main/staging/50900941/command.sh: line 100: scontrol: command not found

Standard Output:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900941/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/50900941/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... mountrepo singularity.galaxyproject.org failed

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

Passed s

jennaj · 2023-06-12T19:03:40Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

jennaj · 2023-06-17T00:01:33Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.4.6+galaxy0

mvdbeek · 2023-06-17T00:16:58Z

Results (powered by Planemo)

Summary

State	Count
Total	8
Passed	8
Error	0
Failure	0
Skipped	0

Passed s

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

Command Line:

Exit Code:

```
0
```

Standard Error:

/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:08:42 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:42 *****
2023-06-16 20:08:42 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:42 INFO:	Mode is genome
2023-06-16 20:08:42 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:51 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/inputs/dataset_eb6a1674-dd1c-4836-ba23-1e7210df35d2.dat
2023-06-16 20:08:51 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:08:58 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:09:06 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:09:06 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:09:06
2023-06-16 20:09:08 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:09:08 INFO:	Running 1 job(s) on makeblastdb, starting at 06/16/2023 20:09:08
2023-06-16 20:09:10 INFO:	Creating BLAST database with input file
2023-06-16 20:09:10 INFO:	[makeblastdb]	1 of 1 task(s) completed
2023-06-16 20:09:10 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:09:10 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:09:10
2023-06-16 20:09:13 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:09:13 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:09:13 INFO:	Running Augustus prediction using fly as species:
2023-06-16 20:09:13 INFO:	Running 4 job(s) on augustus, starting at 06/16/2023 20:09:13
2023-06-16 20:09:18 INFO:	[augustus]	1 of 4 task(s) completed
2023-06-16 20:09:20 INFO:	[augustus]	2 of 4 task(s) completed
2023-06-16 20:09:22 INFO:	[augustus]	3 of 4 task(s) completed
2023-06-16 20:09:25 INFO:	[augustus]	4 of 4 task(s) completed
2023-06-16 20:09:25 INFO:	Extracting predicted proteins...
2023-06-16 20:09:25 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:25 INFO:	Running 4 job(s) on hmmsearch, starting at 06/16/2023 20:09:25
2023-06-16 20:09:27 INFO:	[hmmsearch]	1 of 4 task(s) completed
2023-06-16 20:09:27 INFO:	[hmmsearch]	2 of 4 task(s) completed
2023-06-16 20:09:27 INFO:	[hmmsearch]	3 of 4 task(s) completed
2023-06-16 20:09:27 INFO:	[hmmsearch]	4 of 4 task(s) completed
2023-06-16 20:09:28 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2023-06-16 20:09:28 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2023-06-16 20:09:29 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:09:29 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:09:29
2023-06-16 20:09:44 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:09:44 INFO:	Converting predicted genes to short genbank files
2023-06-16 20:09:44 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 06/16/2023 20:09:44
2023-06-16 20:09:46 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2023-06-16 20:09:46 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2023-06-16 20:09:46 INFO:	Running 1 job(s) on new_species.pl, starting at 06/16/2023 20:09:46
2023-06-16 20:09:48 INFO:	[new_species.pl]	1 of 1 task(s) completed
2023-06-16 20:09:48 INFO:	Running 1 job(s) on etraining, starting at 06/16/2023 20:09:48
2023-06-16 20:09:50 INFO:	[etraining]	1 of 1 task(s) completed
2023-06-16 20:09:50 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
2023-06-16 20:09:50 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:09:50 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2023-06-16 20:09:50 INFO:	Running 18 job(s) on augustus, starting at 06/16/2023 20:09:50
2023-06-16 20:09:53 INFO:	[augustus]	2 of 18 task(s) completed
2023-06-16 20:09:54 INFO:	[augustus]	4 of 18 task(s) completed
2023-06-16 20:09:55 INFO:	[augustus]	6 of 18 task(s) completed
2023-06-16 20:09:57 INFO:	[augustus]	8 of 18 task(s) completed
2023-06-16 20:09:58 INFO:	[augustus]	10 of 18 task(s) completed
2023-06-16 20:09:58 INFO:	[augustus]	11 of 18 task(s) completed
2023-06-16 20:09:59 INFO:	[augustus]	13 of 18 task(s) completed
2023-06-16 20:10:01 INFO:	[augustus]	15 of 18 task(s) completed
2023-06-16 20:10:03 INFO:	[augustus]	17 of 18 task(s) completed
2023-06-16 20:10:04 INFO:	[augustus]	18 of 18 task(s) completed
2023-06-16 20:10:04 INFO:	Extracting predicted proteins...
2023-06-16 20:10:04 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:04 INFO:	Running 18 job(s) on hmmsearch, starting at 06/16/2023 20:10:04
2023-06-16 20:10:06 INFO:	[hmmsearch]	2 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	4 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	6 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	8 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	10 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	11 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	13 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	15 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	17 of 18 task(s) completed
2023-06-16 20:10:06 INFO:	[hmmsearch]	18 of 18 task(s) completed
2023-06-16 20:10:08 INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

2023-06-16 20:10:08 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               |
	--------------------------------------------------
2023-06-16 20:10:08 INFO:	BUSCO analysis done. Total running time: 77 seconds
2023-06-16 20:10:08 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/working/busco_galaxy
2023-06-16 20:10:08 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:10:08 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056326/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 0, "augustus_mode": "no"}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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 Error:

2023-06-16 20:09:03 ERROR:	
Warning message:
package 'ggplot2' was built under R version 4.2.3 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
i Please use the `linewidth` argument instead. 


/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:08:33 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:33 *****
2023-06-16 20:08:33 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:33 INFO:	Mode is proteins
2023-06-16 20:08:33 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:40 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/inputs/dataset_a873ca71-d051-4bb4-8668-f6720bb90f7a.dat
2023-06-16 20:08:40 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:08:48 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:08:53 WARNING:	Option evalue was provided but is not used in the selected run mode, proteins
2023-06-16 20:08:53 WARNING:	Option limit was provided but is not used in the selected run mode, proteins
2023-06-16 20:08:53 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:08:53 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:08:53 INFO:	Running 1013 job(s) on hmmsearch, starting at 06/16/2023 20:08:53
2023-06-16 20:08:55 INFO:	[hmmsearch]	203 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	304 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	406 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	507 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	608 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	710 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	811 of 1013 task(s) completed
2023-06-16 20:08:55 INFO:	[hmmsearch]	912 of 1013 task(s) completed
2023-06-16 20:08:56 INFO:	[hmmsearch]	1013 of 1013 task(s) completed
2023-06-16 20:08:58 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               |
	--------------------------------------------------
2023-06-16 20:08:58 INFO:	BUSCO analysis done with WARNING(s). Total running time: 17 seconds

***** Summary of warnings: *****
2023-06-16 20:08:53 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, proteins
2023-06-16 20:08:53 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, proteins

2023-06-16 20:08:58 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/working/busco_galaxy
2023-06-16 20:08:58 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:08:58 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 10
drwx------ 5 xcgalaxy mcb140028p  4096 Jun 16 20:08 busco_sequences
-rw------- 1 xcgalaxy mcb140028p 20988 Jun 16 20:08 full_table.tsv
drwx------ 4 xcgalaxy mcb140028p  4096 Jun 16 20:08 hmmer_output
-rw------- 1 xcgalaxy mcb140028p 12734 Jun 16 20:08 missing_busco_list.tsv
-rw------- 1 xcgalaxy mcb140028p  1796 Jun 16 20:08 short_summary.json
-rw------- 1 xcgalaxy mcb140028p   692 Jun 16 20:08 short_summary.txt
2023-06-16 20:08:58 INFO:	****************** Start plot generation at 06/16/2023 20:08:58 ******************
2023-06-16 20:08:58 INFO:	Load data ...
2023-06-16 20:08:58 INFO:	Loaded BUSCO_summaries/short_summary.specific.arthropoda_odb10.busco_galaxy.txt successfully
2023-06-16 20:08:58 INFO:	Generate the R code ...
2023-06-16 20:08:58 INFO:	Run the R code ...
2023-06-16 20:09:03 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2023-06-16 20:09:03 INFO:	Plot generation done. Total running time: 5.331966876983643 seconds
2023-06-16 20:09:03 INFO:	Results written in BUSCO_summaries/


CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056325/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 2, "mode": "prot"}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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 Error:

2023-06-16 20:09:41 ERROR:	
Warning message:
package 'ggplot2' was built under R version 4.2.3 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
i Please use the `linewidth` argument instead. 


/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:08:34 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:34 *****
2023-06-16 20:08:34 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:34 INFO:	Mode is transcriptome
2023-06-16 20:08:34 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:42 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/inputs/dataset_afc2b12f-0473-4455-918c-b01b12438356.dat
2023-06-16 20:08:42 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:08:52 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:08:57 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_tran
2023-06-16 20:08:57 WARNING:	Option limit was provided but is not used in the selected run mode, euk_tran
2023-06-16 20:08:57 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:08:58 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:08:58
2023-06-16 20:09:05 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:06 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:06 INFO:	Running 1013 job(s) on hmmsearch, starting at 06/16/2023 20:09:06
2023-06-16 20:09:08 INFO:	[hmmsearch]	102 of 1013 task(s) completed
2023-06-16 20:09:08 INFO:	[hmmsearch]	203 of 1013 task(s) completed
2023-06-16 20:09:08 INFO:	[hmmsearch]	304 of 1013 task(s) completed
2023-06-16 20:09:08 INFO:	[hmmsearch]	406 of 1013 task(s) completed
2023-06-16 20:09:09 INFO:	[hmmsearch]	507 of 1013 task(s) completed
2023-06-16 20:09:09 INFO:	[hmmsearch]	608 of 1013 task(s) completed
2023-06-16 20:09:09 INFO:	[hmmsearch]	811 of 1013 task(s) completed
2023-06-16 20:09:09 INFO:	[hmmsearch]	912 of 1013 task(s) completed
2023-06-16 20:09:09 INFO:	[hmmsearch]	1013 of 1013 task(s) completed
2023-06-16 20:09:12 INFO:	0 candidate overlapping regions found
2023-06-16 20:09:12 INFO:	1 exons in total
2023-06-16 20:09:12 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2023-06-16 20:09:26 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:09:26
2023-06-16 20:09:32 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:32 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:32 INFO:	Running 1012 job(s) on hmmsearch, starting at 06/16/2023 20:09:32
2023-06-16 20:09:34 INFO:	[hmmsearch]	102 of 1012 task(s) completed
2023-06-16 20:09:34 INFO:	[hmmsearch]	203 of 1012 task(s) completed
2023-06-16 20:09:34 INFO:	[hmmsearch]	304 of 1012 task(s) completed
2023-06-16 20:09:34 INFO:	[hmmsearch]	405 of 1012 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	507 of 1012 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	608 of 1012 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	608 of 1012 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	810 of 1012 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	1012 of 1012 task(s) completed
2023-06-16 20:09:36 INFO:	0 candidate overlapping regions found
2023-06-16 20:09:36 INFO:	1 exons in total
2023-06-16 20:09:36 INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

2023-06-16 20:09:36 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               |
	--------------------------------------------------
2023-06-16 20:09:36 INFO:	BUSCO analysis done with WARNING(s). Total running time: 54 seconds

***** Summary of warnings: *****
2023-06-16 20:08:57 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_tran
2023-06-16 20:08:57 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_tran

2023-06-16 20:09:36 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/working/busco_galaxy
2023-06-16 20:09:36 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:09:36 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 14
drwx------ 5 xcgalaxy mcb140028p  4096 Jun 16 20:08 busco_sequences
-rw------- 1 xcgalaxy mcb140028p 20995 Jun 16 20:09 full_table.tsv
drwx------ 4 xcgalaxy mcb140028p  4096 Jun 16 20:09 hmmer_output
drwx------ 4 xcgalaxy mcb140028p  4096 Jun 16 20:09 metaeuk_output
-rw------- 1 xcgalaxy mcb140028p 12734 Jun 16 20:09 missing_busco_list.tsv
-rw------- 1 xcgalaxy mcb140028p  1967 Jun 16 20:09 short_summary.json
-rw------- 1 xcgalaxy mcb140028p   712 Jun 16 20:09 short_summary.txt
2023-06-16 20:09:37 INFO:	****************** Start plot generation at 06/16/2023 20:09:37 ******************
2023-06-16 20:09:37 INFO:	Load data ...
2023-06-16 20:09:37 INFO:	Loaded BUSCO_summaries/short_summary.specific.arthropoda_odb10.busco_galaxy.txt successfully
2023-06-16 20:09:37 INFO:	Generate the R code ...
2023-06-16 20:09:37 INFO:	Run the R code ...
2023-06-16 20:09:41 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2023-06-16 20:09:41 INFO:	Plot generation done. Total running time: 4.172755479812622 seconds
2023-06-16 20:09:41 INFO:	Results written in BUSCO_summaries/


CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056322/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 1, "mode": "tran"}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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:

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/51056328/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/51056328/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /scratch4/nekrut/galaxy/main/staging/51056328/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
2023-06-16 20:08:33 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:33 *****
2023-06-16 20:08:33 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:33 INFO:	Mode is genome
2023-06-16 20:08:33 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:37 INFO:	Input file is /scratch4/nekrut/galaxy/main/staging/51056328/inputs/dataset_eb6a1674-dd1c-4836-ba23-1e7210df35d2.dat
2023-06-16 20:08:37 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:08:43 INFO:	Decompressing file '/scratch4/nekrut/galaxy/main/staging/51056328/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:09:01 WARNING:	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored
2023-06-16 20:09:11 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:09:11 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:09:11
2023-06-16 20:09:25 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:09:25 INFO:	Running 1 job(s) on makeblastdb, starting at 06/16/2023 20:09:25
2023-06-16 20:09:28 INFO:	Creating BLAST database with input file
2023-06-16 20:09:29 INFO:	[makeblastdb]	1 of 1 task(s) completed
2023-06-16 20:09:29 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:09:29 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:09:29
2023-06-16 20:09:33 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:09:33 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:09:33 INFO:	Running Augustus prediction using human as species:
2023-06-16 20:09:33 INFO:	Running 4 job(s) on augustus, starting at 06/16/2023 20:09:33
2023-06-16 20:09:36 INFO:	[augustus]	1 of 4 task(s) completed
2023-06-16 20:09:37 INFO:	[augustus]	2 of 4 task(s) completed
2023-06-16 20:09:38 INFO:	[augustus]	3 of 4 task(s) completed
2023-06-16 20:09:40 INFO:	[augustus]	4 of 4 task(s) completed
2023-06-16 20:09:40 INFO:	Extracting predicted proteins...
2023-06-16 20:09:40 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:40 INFO:	Running 4 job(s) on hmmsearch, starting at 06/16/2023 20:09:40
2023-06-16 20:09:42 INFO:	[hmmsearch]	1 of 4 task(s) completed
2023-06-16 20:09:42 INFO:	[hmmsearch]	2 of 4 task(s) completed
2023-06-16 20:09:42 INFO:	[hmmsearch]	3 of 4 task(s) completed
2023-06-16 20:09:42 INFO:	[hmmsearch]	4 of 4 task(s) completed
2023-06-16 20:09:44 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2023-06-16 20:09:44 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2023-06-16 20:09:45 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:09:45 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:09:45
2023-06-16 20:10:02 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:10:02 INFO:	Converting predicted genes to short genbank files
2023-06-16 20:10:02 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 06/16/2023 20:10:02
2023-06-16 20:10:05 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2023-06-16 20:10:05 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2023-06-16 20:10:05 INFO:	Running 1 job(s) on new_species.pl, starting at 06/16/2023 20:10:05
2023-06-16 20:10:08 INFO:	[new_species.pl]	1 of 1 task(s) completed
2023-06-16 20:10:08 INFO:	Running 1 job(s) on etraining, starting at 06/16/2023 20:10:08
2023-06-16 20:10:10 INFO:	[etraining]	1 of 1 task(s) completed
2023-06-16 20:10:10 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
2023-06-16 20:10:10 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:10:10 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2023-06-16 20:10:10 INFO:	Running 18 job(s) on augustus, starting at 06/16/2023 20:10:10
2023-06-16 20:10:13 INFO:	[augustus]	2 of 18 task(s) completed
2023-06-16 20:10:14 INFO:	[augustus]	4 of 18 task(s) completed
2023-06-16 20:10:15 INFO:	[augustus]	6 of 18 task(s) completed
2023-06-16 20:10:17 INFO:	[augustus]	8 of 18 task(s) completed
2023-06-16 20:10:18 INFO:	[augustus]	10 of 18 task(s) completed
2023-06-16 20:10:19 INFO:	[augustus]	11 of 18 task(s) completed
2023-06-16 20:10:20 INFO:	[augustus]	13 of 18 task(s) completed
2023-06-16 20:10:21 INFO:	[augustus]	15 of 18 task(s) completed
2023-06-16 20:10:23 INFO:	[augustus]	17 of 18 task(s) completed
2023-06-16 20:10:24 INFO:	[augustus]	18 of 18 task(s) completed
2023-06-16 20:10:24 INFO:	Extracting predicted proteins...
2023-06-16 20:10:24 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:24 INFO:	Running 18 job(s) on hmmsearch, starting at 06/16/2023 20:10:24
2023-06-16 20:10:26 INFO:	[hmmsearch]	2 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	4 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	6 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	8 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	10 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	11 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	13 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	15 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	17 of 18 task(s) completed
2023-06-16 20:10:26 INFO:	[hmmsearch]	18 of 18 task(s) completed
2023-06-16 20:10:29 INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

2023-06-16 20:10:29 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               |
	--------------------------------------------------
2023-06-16 20:10:29 INFO:	BUSCO analysis done with WARNING(s). Total running time: 112 seconds

***** Summary of warnings: *****
2023-06-16 20:09:01 WARNING:busco.BuscoConfig	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored

2023-06-16 20:10:29 INFO:	Results written in /scratch4/nekrut/galaxy/main/staging/51056328/working/busco_galaxy
2023-06-16 20:10:29 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:10:29 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 2, "augustus_mode": "builtin", "augustus_species": "human"}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
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 Error:

/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:10:00 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:10:00 *****
2023-06-16 20:10:00 INFO:	Configuring BUSCO with local environment
2023-06-16 20:10:00 INFO:	Mode is genome
2023-06-16 20:10:00 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:10:03 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/inputs/dataset_eb6a1674-dd1c-4836-ba23-1e7210df35d2.dat
2023-06-16 20:10:03 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:10:08 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:10:14 WARNING:	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored
2023-06-16 20:10:17 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:10:17 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:10:17
2023-06-16 20:10:19 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:10:19 INFO:	Running 1 job(s) on makeblastdb, starting at 06/16/2023 20:10:19
2023-06-16 20:10:20 INFO:	Creating BLAST database with input file
2023-06-16 20:10:21 INFO:	[makeblastdb]	1 of 1 task(s) completed
2023-06-16 20:10:21 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:10:21 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:10:21
2023-06-16 20:10:24 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:10:24 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:10:24 INFO:	Running Augustus prediction using local as species:
2023-06-16 20:10:24 INFO:	Running 4 job(s) on augustus, starting at 06/16/2023 20:10:24
2023-06-16 20:10:28 INFO:	[augustus]	1 of 4 task(s) completed
2023-06-16 20:10:31 INFO:	[augustus]	2 of 4 task(s) completed
2023-06-16 20:10:33 INFO:	[augustus]	3 of 4 task(s) completed
2023-06-16 20:10:36 INFO:	[augustus]	4 of 4 task(s) completed
2023-06-16 20:10:36 INFO:	Extracting predicted proteins...
2023-06-16 20:10:36 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:36 INFO:	Running 4 job(s) on hmmsearch, starting at 06/16/2023 20:10:36
2023-06-16 20:10:37 INFO:	[hmmsearch]	1 of 4 task(s) completed
2023-06-16 20:10:37 INFO:	[hmmsearch]	2 of 4 task(s) completed
2023-06-16 20:10:37 INFO:	[hmmsearch]	3 of 4 task(s) completed
2023-06-16 20:10:37 INFO:	[hmmsearch]	4 of 4 task(s) completed
2023-06-16 20:10:39 INFO:	Starting second step of analysis. The gene predictor Augustus is retrained using the results from the initial run to yield more accurate results.
2023-06-16 20:10:39 INFO:	Extracting missing and fragmented buscos from the file ancestral_variants...
2023-06-16 20:10:40 INFO:	Running a BLAST search for BUSCOs against created database
2023-06-16 20:10:40 INFO:	Running 1 job(s) on tblastn, starting at 06/16/2023 20:10:40
2023-06-16 20:10:54 INFO:	[tblastn]	1 of 1 task(s) completed
2023-06-16 20:10:57 INFO:	Converting predicted genes to short genbank files
2023-06-16 20:10:57 INFO:	Running 1 job(s) on gff2gbSmallDNA.pl, starting at 06/16/2023 20:10:57
2023-06-16 20:10:59 INFO:	[gff2gbSmallDNA.pl]	1 of 1 task(s) completed
2023-06-16 20:11:01 INFO:	All files converted to short genbank files, now training Augustus using Single-Copy Complete BUSCOs
2023-06-16 20:11:01 INFO:	Running 1 job(s) on new_species.pl, starting at 06/16/2023 20:11:01
2023-06-16 20:11:03 INFO:	[new_species.pl]	1 of 1 task(s) completed
2023-06-16 20:11:03 INFO:	Running 1 job(s) on etraining, starting at 06/16/2023 20:11:03
2023-06-16 20:11:05 INFO:	[etraining]	1 of 1 task(s) completed
2023-06-16 20:11:05 INFO:	Re-running Augustus with the new metaparameters, number of target BUSCOs: 1012
2023-06-16 20:11:05 INFO:	Running Augustus gene predictor on BLAST search results.
2023-06-16 20:11:05 INFO:	Running Augustus prediction using BUSCO_busco_galaxy as species:
2023-06-16 20:11:05 INFO:	Running 18 job(s) on augustus, starting at 06/16/2023 20:11:05
2023-06-16 20:11:07 INFO:	[augustus]	2 of 18 task(s) completed
2023-06-16 20:11:09 INFO:	[augustus]	4 of 18 task(s) completed
2023-06-16 20:11:10 INFO:	[augustus]	6 of 18 task(s) completed
2023-06-16 20:11:12 INFO:	[augustus]	8 of 18 task(s) completed
2023-06-16 20:11:13 INFO:	[augustus]	10 of 18 task(s) completed
2023-06-16 20:11:13 INFO:	[augustus]	11 of 18 task(s) completed
2023-06-16 20:11:14 INFO:	[augustus]	13 of 18 task(s) completed
2023-06-16 20:11:16 INFO:	[augustus]	15 of 18 task(s) completed
2023-06-16 20:11:18 INFO:	[augustus]	17 of 18 task(s) completed
2023-06-16 20:11:19 INFO:	[augustus]	18 of 18 task(s) completed
2023-06-16 20:11:19 INFO:	Extracting predicted proteins...
2023-06-16 20:11:19 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:11:19 INFO:	Running 18 job(s) on hmmsearch, starting at 06/16/2023 20:11:19
2023-06-16 20:11:21 INFO:	[hmmsearch]	2 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	4 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	6 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	8 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	10 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	11 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	13 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	15 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	17 of 18 task(s) completed
2023-06-16 20:11:21 INFO:	[hmmsearch]	18 of 18 task(s) completed
2023-06-16 20:11:23 INFO:	Results:	C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013	   

2023-06-16 20:11:23 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               |
	--------------------------------------------------
2023-06-16 20:11:23 INFO:	BUSCO analysis done with WARNING(s). Total running time: 80 seconds

***** Summary of warnings: *****
2023-06-16 20:10:14 WARNING:busco.BuscoConfig	An augustus species was mentioned in the config file or on the command line, dataset default species (fly) will be ignored

2023-06-16 20:11:23 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/working/busco_galaxy
2023-06-16 20:11:23 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:11:23 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056327/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "aug_prediction": {"__current_case__": 1, "augustus_mode": "history", "augustus_model": {"values": [{"id": 113238415, "src": "hda"}]}}, "long": false, "use_augustus_selector": "yes"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

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

Command Line:

Exit Code:

```
0
```

Standard Error:

2023-06-16 20:09:45 ERROR:	
Warning message:
package 'ggplot2' was built under R version 4.2.3 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
i Please use the `linewidth` argument instead. 


/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:08:33 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:33 *****
2023-06-16 20:08:33 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:33 INFO:	Mode is genome
2023-06-16 20:08:33 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:41 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/inputs/dataset_eb6a1674-dd1c-4836-ba23-1e7210df35d2.dat
2023-06-16 20:08:41 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/arthropoda_odb10.2020-09-10.tar.gz'
2023-06-16 20:08:50 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/working/busco_downloads/lineages/arthropoda_odb10.tar.gz'
2023-06-16 20:08:57 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:08:57 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:08:57 INFO:	Running BUSCO using lineage dataset arthropoda_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:08:57 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:08:57
2023-06-16 20:09:00 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:09:01 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:09:01
2023-06-16 20:09:06 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:08 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:08 INFO:	Running 1013 job(s) on hmmsearch, starting at 06/16/2023 20:09:08
2023-06-16 20:09:10 INFO:	[hmmsearch]	102 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	203 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	304 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	406 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	507 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	608 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	710 of 1013 task(s) completed
2023-06-16 20:09:10 INFO:	[hmmsearch]	811 of 1013 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	912 of 1013 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	1013 of 1013 task(s) completed
2023-06-16 20:09:13 INFO:	Validating exons and removing overlapping matches
2023-06-16 20:09:14 INFO:	0 candidate overlapping regions found
2023-06-16 20:09:14 INFO:	1 exons in total
2023-06-16 20:09:14 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2023-06-16 20:09:28 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:09:28
2023-06-16 20:09:33 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:35 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:35 INFO:	Running 1012 job(s) on hmmsearch, starting at 06/16/2023 20:09:35
2023-06-16 20:09:37 INFO:	[hmmsearch]	102 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	203 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	304 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	405 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	507 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	608 of 1012 task(s) completed
2023-06-16 20:09:37 INFO:	[hmmsearch]	709 of 1012 task(s) completed
2023-06-16 20:09:38 INFO:	[hmmsearch]	810 of 1012 task(s) completed
2023-06-16 20:09:38 INFO:	[hmmsearch]	911 of 1012 task(s) completed
2023-06-16 20:09:38 INFO:	[hmmsearch]	1012 of 1012 task(s) completed
2023-06-16 20:09:40 INFO:	Validating exons and removing overlapping matches
2023-06-16 20:09:41 INFO:	0 candidate overlapping regions found
2023-06-16 20:09:41 INFO:	4 exons in total
2023-06-16 20:09:41 INFO:	Results:	C:0.2%[S:0.2%,D:0.0%],F:0.0%,M:99.8%,n:1013	   

2023-06-16 20:09:42 INFO:	

	--------------------------------------------------
	|Results from dataset arthropoda_odb10            |
	--------------------------------------------------
	|C:0.2%[S:0.2%,D:0.0%],F:0.0%,M:99.8%,n:1013      |
	|2	Complete BUSCOs (C)                       |
	|2	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|1011	Missing BUSCOs (M)                        |
	|1013	Total BUSCO groups searched               |
	--------------------------------------------------
2023-06-16 20:09:42 INFO:	BUSCO analysis done with WARNING(s). Total running time: 60 seconds

***** Summary of warnings: *****
2023-06-16 20:08:57 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:08:57 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met

2023-06-16 20:09:42 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/working/busco_galaxy
2023-06-16 20:09:42 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:09:42 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 14
drwx------ 5 xcgalaxy mcb140028p  4096 Jun 16 20:08 busco_sequences
-rw------- 1 xcgalaxy mcb140028p 21153 Jun 16 20:09 full_table.tsv
drwx------ 4 xcgalaxy mcb140028p  4096 Jun 16 20:09 hmmer_output
drwx------ 4 xcgalaxy mcb140028p  4096 Jun 16 20:09 metaeuk_output
-rw------- 1 xcgalaxy mcb140028p 12722 Jun 16 20:09 missing_busco_list.tsv
-rw------- 1 xcgalaxy mcb140028p  2311 Jun 16 20:09 short_summary.json
-rw------- 1 xcgalaxy mcb140028p   912 Jun 16 20:09 short_summary.txt
2023-06-16 20:09:42 INFO:	****************** Start plot generation at 06/16/2023 20:09:42 ******************
2023-06-16 20:09:42 INFO:	Load data ...
2023-06-16 20:09:42 INFO:	Loaded BUSCO_summaries/short_summary.specific.arthropoda_odb10.busco_galaxy.txt successfully
2023-06-16 20:09:42 INFO:	Generate the R code ...
2023-06-16 20:09:42 INFO:	Run the R code ...
2023-06-16 20:09:45 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2023-06-16 20:09:45 INFO:	Plot generation done. Total running time: 3.004070281982422 seconds
2023-06-16 20:09:45 INFO:	Results written in BUSCO_summaries/


CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056321/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}`
lineage	`{"__current_case__": 1, "lineage_dataset": "arthropoda_odb10", "lineage_mode": "select_lineage"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

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

Command Line:

Exit Code:

```
0
```

Standard Error:

2023-06-16 20:13:39 ERROR:	
Warning message:
package 'ggplot2' was built under R version 4.2.3 
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
i Please use the `linewidth` argument instead. 


/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/domain.d: No such file or directory
/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/mountrepo: line 70: cd: /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/cvmfs-config.cern.ch/etc/cvmfs/config.d: No such file or directory

Standard Output:

2023-06-16 20:08:41 INFO:	***** Start a BUSCO v5.4.6 analysis, current time: 06/16/2023 20:08:41 *****
2023-06-16 20:08:41 INFO:	Configuring BUSCO with local environment
2023-06-16 20:08:41 INFO:	Mode is genome
2023-06-16 20:08:41 INFO:	Downloading information on latest versions of BUSCO data...
2023-06-16 20:08:50 INFO:	Input file is /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/inputs/dataset_eb6a1674-dd1c-4836-ba23-1e7210df35d2.dat
2023-06-16 20:08:50 INFO:	No lineage specified. Running lineage auto selector.

2023-06-16 20:08:50 INFO:	***** Starting Auto Select Lineage *****
	This process runs BUSCO on the generic lineage datasets for the domains archaea, bacteria and eukaryota. Once the optimal domain is selected, BUSCO automatically attempts to find the most appropriate BUSCO dataset to use based on phylogenetic placement.
	--auto-lineage-euk and --auto-lineage-prok are also available if you know your input assembly is, or is not, an eukaryote. See the user guide for more information.
	A reminder: Busco evaluations are valid when an appropriate dataset is used, i.e., the dataset belongs to the lineage of the species to test. Because of overlapping markers/spurious matches among domains, busco matches in another domain do not necessarily mean that your genome/proteome contains sequences from this domain. However, a high busco score in multiple domains might help you identify possible contaminations.
2023-06-16 20:08:50 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/archaea_odb10.2021-02-23.tar.gz'
2023-06-16 20:08:53 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/archaea_odb10.tar.gz'
2023-06-16 20:08:54 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:08:54 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:08:55 INFO:	Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)
2023-06-16 20:08:55 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:08:55
2023-06-16 20:08:57 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:08:57 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-06-16 20:08:57 INFO:	Running Prodigal with genetic code 11 in meta mode
2023-06-16 20:08:57 INFO:	Running 1 job(s) on prodigal, starting at 06/16/2023 20:08:57
2023-06-16 20:08:59 INFO:	[prodigal]	1 of 1 task(s) completed
2023-06-16 20:08:59 INFO:	Genetic code 11 selected as optimal
2023-06-16 20:08:59 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:08:59 INFO:	Running 194 job(s) on hmmsearch, starting at 06/16/2023 20:08:59
2023-06-16 20:09:01 INFO:	[hmmsearch]	20 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	20 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	39 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	59 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	78 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	97 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	117 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	136 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	156 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	175 of 194 task(s) completed
2023-06-16 20:09:01 INFO:	[hmmsearch]	194 of 194 task(s) completed
2023-06-16 20:09:03 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:09:03 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:194	   

2023-06-16 20:09:03 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz'
2023-06-16 20:09:05 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/bacteria_odb10.tar.gz'
2023-06-16 20:09:06 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:09:06 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:09:06 INFO:	Running BUSCO using lineage dataset bacteria_odb10 (prokaryota, 2020-03-06)
2023-06-16 20:09:06 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:09:06
2023-06-16 20:09:07 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:09:07 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-06-16 20:09:07 INFO:	Running Prodigal with genetic code 4 in meta mode
2023-06-16 20:09:07 INFO:	Running 1 job(s) on prodigal, starting at 06/16/2023 20:09:07
2023-06-16 20:09:09 INFO:	[prodigal]	1 of 1 task(s) completed
2023-06-16 20:09:09 INFO:	Genetic code 4 selected as optimal
2023-06-16 20:09:09 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:09 INFO:	Running 124 job(s) on hmmsearch, starting at 06/16/2023 20:09:09
2023-06-16 20:09:11 INFO:	[hmmsearch]	13 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	25 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	38 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	50 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	63 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	75 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	87 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	100 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	112 of 124 task(s) completed
2023-06-16 20:09:11 INFO:	[hmmsearch]	124 of 124 task(s) completed
2023-06-16 20:09:13 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:09:13 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:124	   

2023-06-16 20:09:13 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/eukaryota_odb10.2020-09-10.tar.gz'
2023-06-16 20:09:19 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/eukaryota_odb10.tar.gz'
2023-06-16 20:09:20 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:09:20 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:09:21 INFO:	Running BUSCO using lineage dataset eukaryota_odb10 (eukaryota, 2020-09-10)
2023-06-16 20:09:21 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:09:21
2023-06-16 20:09:22 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:09:24 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:09:24
2023-06-16 20:09:32 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:33 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:33 INFO:	Running 255 job(s) on hmmsearch, starting at 06/16/2023 20:09:33
2023-06-16 20:09:35 INFO:	[hmmsearch]	26 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	51 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	77 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	102 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	128 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	153 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	179 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	230 of 255 task(s) completed
2023-06-16 20:09:35 INFO:	[hmmsearch]	255 of 255 task(s) completed
2023-06-16 20:09:37 INFO:	Validating exons and removing overlapping matches
2023-06-16 20:09:38 INFO:	0 candidate overlapping regions found
2023-06-16 20:09:38 INFO:	1 exons in total
2023-06-16 20:09:38 INFO:	Results:	C:0.4%[S:0.4%,D:0.0%],F:0.0%,M:99.6%,n:255	   

2023-06-16 20:09:38 INFO:	Extracting missing and fragmented buscos from the file refseq_db.faa...
2023-06-16 20:09:48 INFO:	Running 1 job(s) on metaeuk, starting at 06/16/2023 20:09:48
2023-06-16 20:09:56 INFO:	[metaeuk]	1 of 1 task(s) completed
2023-06-16 20:09:58 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:09:58 INFO:	Running 254 job(s) on hmmsearch, starting at 06/16/2023 20:09:58
2023-06-16 20:09:59 INFO:	[hmmsearch]	26 of 254 task(s) completed
2023-06-16 20:09:59 INFO:	[hmmsearch]	51 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	77 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	102 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	127 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	153 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	178 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	178 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	178 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	229 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	229 of 254 task(s) completed
2023-06-16 20:10:00 INFO:	[hmmsearch]	254 of 254 task(s) completed
2023-06-16 20:10:02 INFO:	Validating exons and removing overlapping matches
2023-06-16 20:10:03 INFO:	0 candidate overlapping regions found
2023-06-16 20:10:03 INFO:	1 exons in total
2023-06-16 20:10:03 INFO:	Results:	C:0.4%[S:0.4%,D:0.0%],F:0.0%,M:99.6%,n:255	   

2023-06-16 20:10:03 INFO:	Running virus detection pipeline
2023-06-16 20:10:03 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/information/virus_datasets.2020-11-26.txt.tar.gz'
2023-06-16 20:10:04 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/information/virus_datasets.2020-11-26.txt.tar.gz'
2023-06-16 20:10:04 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/alphabaculovirus_odb10.2020-11-26.tar.gz'
2023-06-16 20:10:06 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/alphabaculovirus_odb10.tar.gz'
2023-06-16 20:10:07 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:07 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:07 INFO:	Running BUSCO using lineage dataset alphabaculovirus_odb10 (viruses, 2020-11-26)
2023-06-16 20:10:07 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:10:07
2023-06-16 20:10:09 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:10:09 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-06-16 20:10:09 INFO:	Running Prodigal with genetic code 1 in meta mode
2023-06-16 20:10:09 INFO:	Running 1 job(s) on prodigal, starting at 06/16/2023 20:10:09
2023-06-16 20:10:10 INFO:	[prodigal]	1 of 1 task(s) completed
2023-06-16 20:10:10 INFO:	Genetic code 11 selected as optimal
2023-06-16 20:10:10 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:10 INFO:	Running 44 job(s) on hmmsearch, starting at 06/16/2023 20:10:10
2023-06-16 20:10:12 INFO:	[hmmsearch]	5 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	9 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	14 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	18 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	23 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	27 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	31 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	36 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	40 of 44 task(s) completed
2023-06-16 20:10:12 INFO:	[hmmsearch]	44 of 44 task(s) completed
2023-06-16 20:10:14 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:14 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:44	   

2023-06-16 20:10:14 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/alphaherpesvirinae_odb10.2020-11-26.tar.gz'
2023-06-16 20:10:16 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/alphaherpesvirinae_odb10.tar.gz'
2023-06-16 20:10:16 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:16 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:16 INFO:	Running BUSCO using lineage dataset alphaherpesvirinae_odb10 (viruses, 2020-11-26)
2023-06-16 20:10:16 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:10:16
2023-06-16 20:10:18 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:10:18 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-06-16 20:10:18 INFO:	Genetic code 11 selected as optimal
2023-06-16 20:10:18 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:18 INFO:	Running 21 job(s) on hmmsearch, starting at 06/16/2023 20:10:18
2023-06-16 20:10:20 INFO:	[hmmsearch]	3 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	5 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	7 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	9 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	11 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	13 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	15 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	17 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	19 of 21 task(s) completed
2023-06-16 20:10:20 INFO:	[hmmsearch]	21 of 21 task(s) completed
2023-06-16 20:10:22 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:22 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:21	   

2023-06-16 20:10:22 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/aviadenovirus_odb10.2020-11-26.tar.gz'
2023-06-16 20:10:23 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/aviadenovirus_odb10.tar.gz'
2023-06-16 20:10:23 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:23 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:24 INFO:	Running BUSCO using lineage dataset aviadenovirus_odb10 (viruses, 2020-11-26)
2023-06-16 20:10:24 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:10:24
2023-06-16 20:10:25 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:10:25 INFO:	***** Run Prodigal on input to predict and extract genes *****
2023-06-16 20:10:25 INFO:	Genetic code 11 selected as optimal
2023-06-16 20:10:25 INFO:	***** Run HMMER on gene sequences *****
2023-06-16 20:10:25 INFO:	Running 13 job(s) on hmmsearch, starting at 06/16/2023 20:10:25
2023-06-16 20:10:27 INFO:	[hmmsearch]	2 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	4 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	4 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	6 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	7 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	8 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	10 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	11 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	12 of 13 task(s) completed
2023-06-16 20:10:27 INFO:	[hmmsearch]	13 of 13 task(s) completed
2023-06-16 20:10:29 WARNING:	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:29 INFO:	Results:	C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:13	   

2023-06-16 20:10:29 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/lineages/baculoviridae_odb10.2020-11-26.tar.gz'
2023-06-16 20:10:30 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/lineages/baculoviridae_odb10.tar.gz'
2023-06-16 20:10:30 WARNING:	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:30 WARNING:	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:31 INFO:	Running BUSCO using lineage dataset baculoviridae_odb10 (viruses, 2020-11-26)
2023-06-16 20:10:31 INFO:	Running 1 job(s) on bbtools, starting at 06/16/2023 20:10:31
2023-06-16 20:10:32 INFO:	[bbtools]	1 of 1 task(s) completed
2023-06-16 20:10:32 INFO:	***** Run Prodigal o
..
in/staging/51056320/working/busco_downloads/placement_files/list_of_reference_markers.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:27 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
2023-06-16 20:13:28 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/placement_files/tree.eukaryota_odb10.2019-12-16.nwk.tar.gz'
2023-06-16 20:13:28 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:29 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/placement_files/tree_metadata.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:29 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
2023-06-16 20:13:31 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/placement_files/supermatrix.aln.eukaryota_odb10.2019-12-16.faa.tar.gz'
2023-06-16 20:13:32 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:32 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/placement_files/mapping_taxids-busco_dataset_name.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:32 INFO:	Downloading file 'https://busco-data.ezlab.org/v5/data/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:34 INFO:	Decompressing file '/ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_downloads/placement_files/mapping_taxid-lineage.eukaryota_odb10.2019-12-16.txt.tar.gz'
2023-06-16 20:13:34 INFO:	No marker genes were found. Root lineage eukaryota_odb10 is kept
2023-06-16 20:13:34 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:13:34 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:13:34 INFO:	

	--------------------------------------------------
	|Results from dataset eukaryota_odb10             |
	--------------------------------------------------
	|C:0.4%[S:0.4%,D:0.0%],F:0.0%,M:99.6%,n:255       |
	|1	Complete BUSCOs (C)                       |
	|1	Complete and single-copy BUSCOs (S)       |
	|0	Complete and duplicated BUSCOs (D)        |
	|0	Fragmented BUSCOs (F)                     |
	|254	Missing BUSCOs (M)                        |
	|255	Total BUSCO groups searched               |
	--------------------------------------------------
2023-06-16 20:13:34 INFO:	BUSCO analysis done with WARNING(s). Total running time: 283 seconds

***** Summary of warnings: *****
2023-06-16 20:08:54 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:08:54 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:09:03 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:09:06 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:09:06 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:09:13 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:09:20 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:09:20 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:10:07 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:07 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:14 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:16 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:16 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:22 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:23 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:23 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:29 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:30 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:30 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:36 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:38 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:38 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:44 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:46 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:46 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:52 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:10:53 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:53 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:10:59 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:01 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:01 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:07 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:08 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:08 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:14 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:16 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:16 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:21 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:23 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:23 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:28 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:30 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:30 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:36 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:38 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:38 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:43 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:45 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:45 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:50 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:52 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:52 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:57 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:11:59 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:11:59 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:05 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:06 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:06 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:12 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:13 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:13 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:19 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:20 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:20 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:26 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:28 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:28 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:34 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:35 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:35 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:41 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:42 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:42 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:48 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:50 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:50 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:56 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:12:57 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:12:57 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:03 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:13:04 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:04 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:10 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:13:12 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:12 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:17 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:13:19 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:19 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, prok_genome
2023-06-16 20:13:25 WARNING:busco.busco_tools.hmmer	BUSCO did not find any match. Make sure to check the log files if this is unexpected.
2023-06-16 20:13:34 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_met
2023-06-16 20:13:34 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_met

2023-06-16 20:13:34 INFO:	Results written in /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/working/busco_galaxy
2023-06-16 20:13:34 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2023-06-16 20:13:34 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 40
drwx------ 5 xcgalaxy mcb140028p 4096 Jun 16 20:09 busco_sequences
-rw------- 1 xcgalaxy mcb140028p 5730 Jun 16 20:10 full_table.tsv
drwx------ 4 xcgalaxy mcb140028p 4096 Jun 16 20:09 hmmer_output
drwx------ 4 xcgalaxy mcb140028p 4096 Jun 16 20:10 metaeuk_output
-rw------- 1 xcgalaxy mcb140028p 3589 Jun 16 20:10 missing_busco_list.tsv
drwx------ 2 xcgalaxy mcb140028p 4096 Jun 16 20:13 placement_files
drwx------ 2 xcgalaxy mcb140028p 4096 Jun 16 20:13 sepp_tmp_files
-rw------- 1 xcgalaxy mcb140028p 2333 Jun 16 20:10 short_summary.json
-rw------- 1 xcgalaxy mcb140028p  924 Jun 16 20:10 short_summary.txt
2023-06-16 20:13:34 INFO:	****************** Start plot generation at 06/16/2023 20:13:34 ******************
2023-06-16 20:13:34 INFO:	Load data ...
2023-06-16 20:13:34 INFO:	Loaded BUSCO_summaries/short_summary.specific.eukaryota_odb10.busco_galaxy.txt successfully
2023-06-16 20:13:34 INFO:	Generate the R code ...
2023-06-16 20:13:34 INFO:	Run the R code ...
2023-06-16 20:13:39 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2023-06-16 20:13:39 INFO:	Plot generation done. Total running time: 4.4719507694244385 seconds
2023-06-16 20:13:39 INFO:	Results written in BUSCO_summaries/


CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
CernVM-FS: loading Fuse module... done
CernVM-FS: mounted cvmfs on /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/data.galaxyproject.org
Unmounting /ocean/projects/mcb140028p/xcgalaxy/main/staging/51056320/.cvmfsexec/dist/cvmfs/singularity.galaxyproject.org

Traceback:

Job Parameters:

Job parameter	Parameter value
lineage_conditional	`{"__current_case__": 1, "selector": "download"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 0, "use_augustus_selector": "no"}}`
lineage	`{"__current_case__": 0, "auto_lineage": "--auto-lineage", "lineage_mode": "auto_detect"}`
outputs	`["short_summary", "missing", "image", "gff"]`
adv	`{"evalue": "0.001", "limit": "3"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

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test busco 5.4.6+galaxy0 #95

test busco 5.4.6+galaxy0 #95

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mvdbeek commented Jun 17, 2023

test busco 5.4.6+galaxy0 #95

test busco 5.4.6+galaxy0 #95

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