jennaj commented 1 year ago

toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863734/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863734/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863734/command.sh: line 110: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47863734/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107239615, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107239625, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863736/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863736/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863736/command.sh: line 110: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47863736/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107239615, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107239625, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863731/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863731/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863731/command.sh: line 110: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47863731/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1878979, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/047/863/47863703/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/047/863/47863703/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/047/863/47863703/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/047/863/47863703/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863738/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863738/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863738/command.sh: line 110: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47863738/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107239615, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107239625, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863740/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863740/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863740/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47863740/command.sh: line 110: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47863740/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107239615, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107239625, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899514/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899514/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899514/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/047/899/47899514/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107315170, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107315175, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899515/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899515/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899515/command.sh: line 110: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47899515/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107315170, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107315175, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899508/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899508/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899508/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/047/899/47899508/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1882277, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899512/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899512/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899512/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/047/899/47899512/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899507/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899507/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/047/899/47899507/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/047/899/47899507/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107315170, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107315175, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899516/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899516/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899516/command.sh: line 110: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /jetstream2/scratch/main/jobs/47899516/command.sh: line 110: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /jetstream2/scratch/main/jobs/47899516/command.sh: line 110: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107315170, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107315175, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": "false", "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": "false", "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": "false", "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

jennaj commented 1 year ago

Update ReRun at org in an account that would hit a non-local cluster. All runs failed. :/ https://usegalaxy.org/u/usinggalaxy2/h/test-unicycler-fastqsangergz

Original Running new tests with tutorial data. All success. Two runs per server -- comparing fastqsanger and fastqsangergz read inputs.

EU: https://usegalaxy.eu/u/jenj/h/test-unicycler-fastqsangergz vs ORG: https://usegalaxy.org/u/jen-galaxyproject/h/test-unicycler-fastqsangergz ORG2: https://usegalaxy.org/u/usinggalaxy2/h/test-unicycler-fastqsangergz (trying to hit jetstream) << all of these failed.

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220137/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220137/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220137/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220137/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944231, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944239, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220166/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220166/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220166/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220166/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944231, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944239, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220136/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220136/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220136/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220136/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1913137, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220169/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220169/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220169/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220169/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220138/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220138/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220138/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220138/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944231, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944239, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220163/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220163/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220163/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220163/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220163/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944231, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944239, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220195/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220195/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220195/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220195/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944308, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944314, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220202/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220202/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220202/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220202/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944308, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944314, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220200/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220200/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220200/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220200/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1913143, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220197/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220197/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220197/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220197/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220196/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220196/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220196/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220196/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944308, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944314, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220199/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220199/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220199/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/220/48220199/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/220/48220199/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 107944308, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 107944314, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269728/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269728/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269728/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/269/48269728/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108045516, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108045522, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269593/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269593/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269593/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/269/48269593/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108045516, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108045522, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1917860, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269571/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269571/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269571/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/269/48269571/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108045516, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108045522, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269604/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269604/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269604/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/269/48269604/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/269/48269604/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108045516, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108045522, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

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

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108084087, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108084094, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108084087, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108084094, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1919309, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290308/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290308/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290308/tool_script.sh: line 10: unicycler: command not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/290/48290308/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290316/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290316/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: /corral4/main/jobs/048/290/48290316/tool_script.sh: line 10: unicycler: command not found . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/048/290/48290316/tool_script.sh: line 10: unicycler: command not found ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108084087, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108084094, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1, exit_code: 127, stderr: . ``` * ``` Output collection 'spades_collection': expected to have 14 elements, but it had 0. ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108084087, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108084094, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)
**Problems**: * ``` 'command_line' ```

jennaj commented 1 year ago

Reruns in here https://usegalaxy.org/u/usinggalaxy2/h/technical-test-unicycler

jennaj commented 1 year ago

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.0+galaxy1

mvdbeek commented 1 year ago

Results (powered by Planemo)

Summary

State	Count
Total	7
Passed	6
Error	0
Failure	1
Skipped	0

Failed s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #7)

**Problems**: * ``` 'command_line' ```

Passed s

*

✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #1)

**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108184204, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108184210, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #2)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Starting Unicycler (2023-02-10 14:04:24) Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you provided both short and long reads, Unicycler will perform a hybrid assembly. It will first use SPAdes to make a short-read assembly graph, and then it will use various methods to scaffold that graph with the long reads. For more information, please see https://github.com/rrwick/Unicycler Command: /usr/local/bin/unicycler -t 6 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0 Unicycler version: v0.5.0 Using 6 threads The output directory already exists and files may be reused or overwritten: /corral4/main/jobs/048/338/48338891/working Bridging mode: normal using default normal bridge quality cutoff: 10.00 Dependencies: Program Version Status Path spades.py 3.15.5 good /usr/local/bin/spades.py racon 1.5.0 good /usr/local/bin/racon makeblastdb 2.13.0+ good /usr/local/bin/makeblastdb tblastn 2.13.0+ good /usr/local/bin/tblastn Choosing k-mer range for assembly (2023-02-10 14:04:26) Unicycler chooses a k-mer range for SPAdes based on the length of the input reads. It uses a wide range of many k-mer sizes to maximise the chance of finding an ideal assembly. SPAdes maximum k-mer: 127 Median read length: 251 K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127 SPAdes assemblies (2023-02-10 14:04:27) Unicycler now uses SPAdes to assemble the short reads. It scores the assembly graph for each k-mer using the number of contigs (fewer is better) and the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), where c is the contig count and d is the dead end count. spades.py -o /corral4/main/jobs/048/338/48338891/working/spades_assembly -k 27 --threads 6 --isolate -1 /corral4/main/jobs/048/338/48338891/working/fq1.fastq -2 /corral4/main/jobs/048/338/48338891/working/fq2.fastq -m 1024 == Warning == output dir is not empty! Please, clean output directory before run. Command: /usr/local/bin/spades.py -o /corral4/main/jobs/048/338/48338891/working/spades_assembly -k 27 --threads 6 --isolate -1 /corral4/main/jobs/048/338/48338891/working/fq1.fastq -2 /corral4/main/jobs/048/338/48338891/working/fq2.fastq -m 1024 System information: SPAdes version: 3.15.5 Python version: 3.8.13 OS: Linux-3.10.0-1062.18.1.el7.x86_64-x86_64-with-glibc2.10 Output dir: /corral4/main/jobs/048/338/48338891/working/spades_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Isolate mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/corral4/main/jobs/048/338/48338891/working/fq1.fastq'] right reads: ['/corral4/main/jobs/048/338/48338891/working/fq2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: [27] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /corral4/main/jobs/048/338/48338891/working/spades_assembly/tmp Threads: 6 Memory limit (in Gb): 1024 ======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/048/338/48338891/working/spades_assembly/spades.log /corral4/main/jobs/048/338/48338891/working/fq1.fastq: max reads length: 251 /corral4/main/jobs/048/338/48338891/working/fq2.fastq: max reads length: 251 Reads length: 251 ===== Before start started. ===== Assembling started. ===== K27 started. == Running: /usr/local/bin/spades-core /corral4/main/jobs/048/338/48338891/working/spades_assembly/K27/configs/config.info /corral4/main/jobs/048/338/48338891/working/spades_assembly/K27/configs/isolate_mode.info 0:00:00.000 1M / 26M INFO General (main.cpp : 99) Loaded config from /corral4/main/jobs/048/338/48338891/working/spades_assembly/K27/configs/config.info 0:00:00.008 1M / 26M INFO General (main.cpp : 99) Loaded config from /corral4/main/jobs/048/338/48338891/working/spades_assembly/K27/configs/isolate_mode.info 0:00:00.008 1M / 26M INFO General (memory_limit.cpp : 54) Memory limit set to 1024 Gb 0:00:00.012 1M / 26M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 0:00:00.015 1M / 26M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.019 1M / 26M INFO General (main.cpp : 109) Assembling dataset (/corral4/main/jobs/048/338/48338891/working/spades_assembly/dataset.info) with K=27 0:00:00.023 1M / 26M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 6 0:00:00.026 1M / 26M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.030 1M / 26M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.033 1M / 26M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.040 1M / 26M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.042 1M / 26M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.047 1M / 26M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:00.052 1M / 26M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.056 1M / 26M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.060 1M / 26M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.062 1M / 26M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.174 63M / 63M INFO General (binary_converter.cpp : 111) 7925 reads written 0:00:00.180 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 0:00:00.186 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.190 41M / 41M INFO General (read_converter.cpp : 92) Converting merged reads 0:00:00.196 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.220 1M / 26M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.231 1M / 26M INFO General (construction.cpp : 153) Max read length 251 0:00:00.234 1M / 26M INFO General (construction.cpp : 159) Average read length 250.525 0:00:00.238 1M / 26M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.242 1M / 26M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 60 files using 6 threads. This might take a while. 0:00:00.251 1M / 26M INFO General (file_limit.hpp : 42) Open file limit set to 131072 0:00:00.255 1M / 26M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 56.8889 Gb 0:00:00.255 1M / 26M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118481 0:00:00.672 1M / 707M INFO General (kmer_splitters.hpp : 131) Used 31700 reads 0:00:00.676 1M / 707M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:00.842 1M / 707M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 35249 kmers in total. 0:00:00.846 1M / 707M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:00.873 1M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:00.874 1M / 707M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 60 files using 6 threads. This might take a while. 0:00:00.877 1M / 707M INFO General (file_limit.hpp : 42) Open file limit set to 131072 0:00:00.877 1M / 707M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 56.8889 Gb 0:00:00.878 1M / 707M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118481 0:00:01.167 3601M / 3601M INFO General (kmer_splitters.hpp : 194) Processed 35249 kmers 0:00:01.175 3601M / 3601M INFO General (kmer_splitters.hpp : 199) Used 35249 kmers. 0:00:01.180 1M / 707M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:01.375 1M / 707M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 34510 kmers in total. 0:00:01.380 1M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.404 1M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 34510 kmers, 71424 bytes occupied (16.5573 bits per kmer). 0:00:01.408 1M / 707M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:00:01.518 1M / 707M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:00:01.531 1M / 707M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:00:01.537 1M / 707M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:00:01.543 1M / 707M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:01.558 1M / 707M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2775 sequences extracted 0:00:01.568 1M / 707M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:01.576 1M / 707M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:01.582 1M / 707M INFO General (debruijn_graph_constructor: 487) Total 5550 edges to create 0:00:01.585 1M / 707M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:00:01.594 1M / 707M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:00:01.601 1M / 707M INFO General (debruijn_graph_constructor: 493) Sorting done 0:00:01.601 1M / 707M INFO General (debruijn_graph_constructor: 503) Total 2036 vertices to create 0:00:01.602 2M / 707M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:00:01.604 1M / 707M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:00:01.605 1M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:01.621 2M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 35249 kmers, 71912 bytes occupied (16.3209 bits per kmer). 0:00:01.622 2M / 707M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:00:01.730 2M / 707M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:00:01.733 2M / 707M INFO General (coverage_filling.hpp : 82) Processed 5550 edges 0:00:01.778 1M / 707M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:00:01.779 1M / 707M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:00:01.779 1M / 707M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695 0:00:01.779 1M / 707M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212 0:00:01.780 1M / 707M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:01.930 1M / 707M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:02.301 1M / 707M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:03.257 1M / 707M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:04.203 1M / 707M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:05.699 1M / 707M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:05.700 1M / 707M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418 0:00:05.702 1M / 707M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:00:05.702 1M / 707M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275 0:00:05.702 1M / 707M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275 0:00:05.702 1M / 707M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132 0:00:05.702 1M / 707M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 671.577 0:00:05.702 1M / 707M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 275 0:00:05.703 1M / 707M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:00:05.703 1M / 707M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:00:05.711 10M / 707M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:05.712 10M / 707M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 415 out of 5550, length: 7516 0:00:05.712 10M / 707M INFO General (edge_index.hpp : 167) Using small index (max_id = 5580) 0:00:05.714 10M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:05.715 10M / 707M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7516 kmers, 6184 byte .. junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k077_assembly_graph.gfa Cleaning k89 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k089_assembly_graph.gfa Cleaning k99 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k099_assembly_graph.gfa Cleaning k107 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k107_assembly_graph.gfa Cleaning k115 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k115_assembly_graph.gfa Cleaning k121 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k121_assembly_graph.gfa Cleaning k127 graph Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k127_assembly_graph.gfa Repair multi way junctions (2023-02-10 14:06:59) Filter by read depth (2023-02-10 14:06:59) Filter homopolymer loops (2023-02-10 14:06:59) Merge all possible (2023-02-10 14:06:59) Normalise read depths (2023-02-10 14:06:59) Remove zero length segments (2023-02-10 14:06:59) Sort link order (2023-02-10 14:06:59) Graph cleaning finished (2023-02-10 14:06:59) Saving /corral4/main/jobs/048/338/48338891/working/spades_assembly/k27_assembly_graph.gfa SPAdes assembly graph summary (2023-02-10 14:06:59) K-mer Contigs Links Total length N50 Longest contig Dead ends Score 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best 47 1 1 5,433 5,433 5,433 0 5.00e-01 63 1 1 5,449 5,449 5,449 0 5.00e-01 77 1 1 5,463 5,463 5,463 0 5.00e-01 89 1 1 5,475 5,475 5,475 0 5.00e-01 99 1 1 5,485 5,485 5,485 0 5.00e-01 107 1 1 5,493 5,493 5,493 0 5.00e-01 115 1 1 5,501 5,501 5,501 0 5.00e-01 121 1 1 5,507 5,507 5,507 0 5.00e-01 127 1 1 5,513 5,513 5,513 0 5.00e-01 Read depth filter: removed 0 contigs totalling 0 bp Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k027.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k047.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k063.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k077.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k089.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k099.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k107.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k115.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k121.gfa Deleting /corral4/main/jobs/048/338/48338891/working/001_spades_graph_k127.gfa Deleting /corral4/main/jobs/048/338/48338891/working/spades_assembly/ Determining graph multiplicity (2023-02-10 14:07:00) Multiplicity is the number of times a sequence occurs in the underlying sequence. Single-copy contigs (those with a multiplicity of one, occurring only once in the underlying sequence) are particularly useful. Multiplicity determination begins by identifying contigs which are clearly single-copy because they are of low depth and do not have more than one link per side. Median depth of 10 longest contigs: 1.00 Initial single copy segments: 1 Unicycler now uses a greedy algorithm to propagate multiplicity through the graph. For example, if two single-copy contigs merge together, the resulting contig will get a multiplicity of two. When no more propagation is possible, additional single-copy contigs are added and the process is repeated. This allows for multiplicity to be correctly assigned to the chromosome (at the median depth) but also for plasmids (which may be higher or lower in depth). MERGING MULTIPLICITY SPLITTING MULTIPLICITY FINDING NEW SINGLE-COPY MERGING MULTIPLICITY SPLITTING MULTIPLICITY REMOVING PROPAGATION TOLERANCE MERGING MULTIPLICITY SPLITTING MULTIPLICITY Cleaning graph (2023-02-10 14:07:00) Unicycler now performs various cleaning procedures on the graph to remove overlaps and simplify the graph structure. The end result is a graph ready for bridging. Grouping graph edges based on overlap removal 0 / 2 (0.0%) 1 / 2 (50.0%) 2 / 2 (100.0%) Removing graph overlaps Bases Bases trimmed trimmed Segment from from number start end 1 13 14 Graph overlaps removed Unicycler now selects a set of anchor contigs from the single-copy contigs. These are the contigs which will be connected via bridges to form the final assembly. 1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp) Anchor segments: 1 Creating SPAdes contig bridges (2023-02-10 14:07:00) SPAdes uses paired-end information to perform repeat resolution (RR) and produce contigs from the assembly graph. SPAdes saves the graph paths corresponding to these contigs in the contigs.paths file. When one of these paths contains two or more anchor contigs, Unicycler can create a bridge from the path. No SPAdes contig bridges Creating loop unrolling bridges (2023-02-10 14:07:00) When a SPAdes contig path connects an anchor contig with the middle contig of a simple loop, Unicycler concludes that the sequences are contiguous (i.e. the loop is not a separate piece of DNA). It then uses the read depth of the middle and repeat contigs to guess the number of times to traverse the loop and makes a bridge. No loop unrolling bridges made none found Loading reads (2023-02-10 14:07:00) 0 / 1 (0.0%) 1 / 1 (100.0%) - 5,386 bp 1 / 1 (100.0%) - 5,386 bp Assembling contigs and long reads with miniasm (2023-02-10 14:07:00) Unicycler uses miniasm to construct a string graph assembly using both the short read contigs and the long reads. It will then use the resulting string graph to produce bridges between contigs. This method requires decent coverage of long reads and therefore may not be fruitful if long reads are sparse. However, it does not rely on the short read assembly graph having good connectivity and is able to bridge an assembly graph even when it contains many dead ends. Unicycler uses two types of "reads" as assembly input: anchor contigs from the short-read assembly and actual long reads which overlap two or more of these contigs. It then assembles them with miniasm. Aligning long reads to graph using minimap Saving /corral4/main/jobs/048/338/48338891/working/miniasm_assembly/all_segments.fasta 1 5386 3 5158 + 1 5386 227 5382 5155 5155 255 cm:i:1149 1 5386 5163 5383 + 1 5386 1 221 220 220 255 cm:i:47 Number of minimap alignments: 1 Saving to /corral4/main/jobs/048/338/48338891/working/miniasm_assembly/01_assembly_reads.fastq: 0 short-read contigs 1 long reads Finding overlaps with minimap... failed Assembling reads with miniasm... empty result Creating simple long read bridges (2023-02-10 14:07:00) Unicycler uses long read alignments (from minimap) to resolve simple repeat structures in the graph. This takes care of some "low-hanging fruit" of the graph simplification. Aligning long reads to graph using minimap Saving /corral4/main/jobs/048/338/48338891/working/simple_bridging/all_segments.fasta 1 5386 3 5158 + 1 5386 227 5382 5155 5155 255 cm:i:1149 1 5386 5163 5383 + 1 5386 1 221 220 220 255 cm:i:47 Number of minimap alignments: 1 Two-way junctions are defined as cases where two graph contigs (A and B) join together (C) and then split apart again (D and E). This usually represents a simple 2-copy repeat, and there are two possible options for its resolution: (A->C->D and B->C->E) or (A->C->E and B->C->D). Each read which spans such a junction gets to "vote" for option 1, option 2 or neither. Unicycler creates a bridge at each junction for the most voted for option. No suitable two-way junctions present Simple loops are parts of the graph where two contigs (A and B) are connected via a repeat (C) which loops back to itself (via D). It is possible to traverse the loop zero times (A->C->B), one time (A->C->D->C->B), two times (A->C->D->C->D->C->B), etc. Long reads which span the loop inform which is the correct number of times through. In this step, such reads are found and each is aligned against alternative loop counts. A reads casts its "vote" for the loop count it agrees best with, and Unicycler creates a bridge using the most voted for count. No suitable simple loops present Determining low score threshold (2023-02-10 14:07:00) Before conducting semi-global alignment of the long reads to the assembly graph, Unicycler must determine a minimum alignment score threshold such that nonsense alignments are excluded. To choose a threshold automatically, it examines alignments between random sequences and selects a score a few standard deviations above the mean. Automatically choosing a threshold using random alignment scores. Random alignment mean score: 61.66 standard deviation: 1.31 Low score threshold: 61.66 + (7 x 1.31) = 70.86 Aligning reads with minimap (2023-02-10 14:07:00) 1 5386 5 5161 + 1 5386 229 5385 5156 5156 255 cm:i:959 1 5386 5168 5384 + 1 5386 6 222 216 216 255 cm:i:39 Done! 1 out of 1 reads aligned Aligning reads (2023-02-10 14:07:00) 1/1: 1 (5386 bp) minimap alignments: 5,5161,+,1,229,5385 5168,5384,+,1,6,222 Reference ranges: 1+: 0 - 5386 Range: 1: 0 - 5386 common 10-mers: 5464 line 1: 215 points, score=213.009259 (good) line 2: 5153 points, score=5151.000388 (good) All Seqan alignments (time to align = 0.093 s): Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 0 224 5162 5386 + 672 100.00 100.00% 1 224 5386 0 5162 + 15486 100.00 100.00% Final alignments: Ref name Ref start Ref end Read start Read end Strand Raw score Scaled score Identity 1 224 5386 0 5162 + 15486 100.00 100.00% 1 0 224 5162 5386 + 672 100.00 100.00% Read alignment summary (2023-02-10 14:07:00) Total read count: 1 Fully aligned reads: 1 Partially aligned reads: 0 Unaligned reads: 0 Total bases aligned: 5,386 bp Mean alignment identity: 100.0% Deleting /corral4/main/jobs/048/338/48338891/working/read_alignment/ Setting the minimum scaled score to the 5.0th percentile of full read alignments: 0.00 Building long read bridges (2023-02-10 14:07:00) Unicycler uses the long read alignments to produce bridges between anchor segments. These bridges can be formed using as few as one long read, giving Unicycler the ability to bridge the graph even when long-read depth is low. Median depth of 10 longest contigs: 1.00 Consensus Consensus Target Search Path Best path Best path Best path Best path Start -> end Reads len (bp) time (s) len (bp) Search type time (s) count Best path len (bp) raw score scaled score length disc Quality Applying bridges (2023-02-10 14:07:00) Unicycler now applies to the graph in decreasing order of quality. This ensures that when multiple, contradictory bridges exist, the most supported option is used. Bridge type Start -> end Path Quality Result Cleaning up leftover segments (2023-02-10 14:07:00) Segments eligible for deletion: Bridged assembly graph (2023-02-10 14:07:00) The assembly is now mostly finished and no more structural changes will be made. Ideally the assembly graph should now have one contig per replicon and no erroneous contigs (i.e. a complete assembly). If there are more contigs, then the assembly is not complete. Component Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 complete Rotating completed replicons (2023-02-10 14:07:00) Any completed circular contigs (i.e. single contigs which have one link connecting end to start) can have their start position changed without altering the sequence. For consistency, Unicycler now searches for a starting gene (dnaA or repA) in each such contig, and if one is found, the contig is rotated to start with that gene on the forward strand. Segment 1: makeblastdb -dbtype nucl -in replicon.fasta tblastn -db replicon.fasta -query /usr/local/lib/python3.8/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1 Segment Length Depth Starting gene Position Strand Identity Coverage 1 5,386 1.00x none found Assembly complete (2023-02-10 14:07:17) Saving /corral4/main/jobs/048/338/48338891/working/assembly.gfa Saving /corral4/main/jobs/048/338/48338891/working/assembly.fasta ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108184204, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108184210, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #3)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 1, "fastq_input1": {"values": [{"id": 1921299, "src": "hdca"}]}, "fastq_input_selector": "paired_collection"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #4)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Starting Unicycler (2023-02-10 14:00:50) Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you provided only long reads, Unicycler will assemble the reads with miniasm and then run repeated polishing rounds using Racon. For more information, please see https://github.com/rrwick/Unicycler Command: /usr/local/bin/unicycler -t 6 -o ./ --verbosity 3 -l lr.fasta --mode normal --min_fasta_length 100 --linear_seqs 0 --min_anchor_seg_len 10 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmers 21,23 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 0 Unicycler version: v0.5.0 Using 6 threads The output directory already exists and files may be reused or overwritten: /corral4/main/jobs/048/338/48338881/working Dependencies: Program Version Status Path spades.py not used racon 1.5.0 good /usr/local/bin/racon makeblastdb 2.13.0+ good /usr/local/bin/makeblastdb tblastn 2.13.0+ good /usr/local/bin/tblastn Loading reads (2023-02-10 14:00:51) 0 / 40 (0.0%) 1 / 40 (2.5%) - 412 bp 2 / 40 (5.0%) - 4,847 bp 3 / 40 (7.5%) - 8,974 bp 4 / 40 (10.0%) - 13,249 bp 5 / 40 (12.5%) - 14,258 bp 6 / 40 (15.0%) - 14,806 bp 7 / 40 (17.5%) - 19,262 bp 8 / 40 (20.0%) - 19,737 bp 9 / 40 (22.5%) - 20,395 bp 10 / 40 (25.0%) - 32,024 bp 11 / 40 (27.5%) - 32,698 bp 12 / 40 (30.0%) - 34,509 bp 13 / 40 (32.5%) - 39,018 bp 14 / 40 (35.0%) - 43,351 bp 15 / 40 (37.5%) - 44,224 bp 16 / 40 (40.0%) - 45,978 bp 17 / 40 (42.5%) - 46,402 bp 18 / 40 (45.0%) - 61,596 bp 19 / 40 (47.5%) - 62,279 bp 20 / 40 (50.0%) - 63,700 bp 21 / 40 (52.5%) - 66,412 bp 22 / 40 (55.0%) - 66,845 bp 23 / 40 (57.5%) - 67,316 bp 24 / 40 (60.0%) - 69,428 bp 25 / 40 (62.5%) - 73,964 bp 26 / 40 (65.0%) - 75,608 bp 27 / 40 (67.5%) - 80,223 bp 28 / 40 (70.0%) - 84,810 bp 29 / 40 (72.5%) - 92,076 bp 30 / 40 (75.0%) - 92,832 bp 31 / 40 (77.5%) - 92,939 bp 32 / 40 (80.0%) - 93,532 bp 33 / 40 (82.5%) - 96,370 bp 34 / 40 (85.0%) - 100,656 bp 35 / 40 (87.5%) - 119,222 bp 36 / 40 (90.0%) - 123,827 bp 37 / 40 (92.5%) - 155,106 bp 38 / 40 (95.0%) - 156,254 bp 39 / 40 (97.5%) - 157,993 bp 40 / 40 (100.0%) - 162,406 bp 40 / 40 (100.0%) - 162,406 bp Assembling contigs and long reads with miniasm (2023-02-10 14:00:51) Saving to /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/01_assembly_reads.fastq: 40 long reads Finding overlaps with minimap... success 120 overlaps Assembling reads with miniasm... success 7 segments, 6 links Unicycler removes any links from the string graph which create branches. I.e. if any segment has two or more links connected to one end, those links are removed. This will result in a graph with only simple linear paths that is suitable for creating unambiguous bridges. No links needed removal Saving /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/11_branching_paths_removed.gfa Merging segments into unitigs: Linear unitig: 3708:125-4288- -> f49b:293-4469+ -> 9e6d:143-4411- -> 9780:142-4271- -> a53e:333-4400+ -> b949:140-4359- -> 054c:932-4389- 1 linear unitig total size = 5,836 bp Saving /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/12_unitig_graph.gfa Polishing miniasm assembly with Racon (2023-02-10 14:00:51) Unicycler now uses Racon to polish the miniasm assembly. It does multiple rounds of polishing to get the best consensus. Circular unitigs are rotated between rounds such that all parts (including the ends) are polished well. Saving to /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/racon_polish/polishing_reads.fastq: 40 long reads Polish Assembly Mapping round size quality 0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template 4286 210 4010 + 1 5836 1061 4603 1147 3800 255 cm:i:200 0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template 4286 129 722 + 1 5836 5221 5833 179 612 255 cm:i:27 054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template 4413 934 4391 - 1 5836 2376 5833 3457 3457 255 cm:i:1153 054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template 4413 126 2525 - 1 5836 30 2314 787 2399 255 cm:i:144 3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template 4605 280 4284 - 1 5836 4 3936 1481 4004 255 cm:i:246 3708cda9-3400-4482-b378-0644f4868ccc_Basecall_1D_template 4605 2719 4286 - 1 5836 4215 5833 546 1618 255 cm:i:88 4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template 4127 170 4027 + 1 5836 1680 5833 1032 4153 255 cm:i:174 4850ae22-4e87-4dbf-83ee-c13cc2c33f9e_Basecall_1D_template 4127 2893 4082 + 1 5836 4 1602 220 1598 255 cm:i:30 598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template 4587 1334 4566 - 1 5836 2699 5786 1281 3232 255 cm:i:243 598f0c09-1917-4ee2-ac23-f021e152cfbf_Basecall_1D_template 4587 98 2778 - 1 5836 50 2663 772 2680 255 cm:i:129 771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template 4615 1225 4611 - 1 5836 2657 5833 1469 3386 255 cm:i:268 771b73f3-1234-4c52-bb54-14c89e6e5e17_Basecall_1D_template 4615 97 2786 - 1 5836 30 2636 905 2689 255 cm:i:157 9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template 4333 143 4271 - 1 5836 338 4254 1834 4128 255 cm:i:470 9780e420-c7e3-4229-b406-d3d4b590ab2d_Basecall_1D_template 4333 3092 4330 - 1 5836 4503 5798 430 1295 255 cm:i:77 9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template 4536 544 4408 - 1 5836 69 3927 1208 3864 255 cm:i:237 9e6d95e5-24f9-43ca-b3a0-4989848e3005_Basecall_1D_template 4536 3008 4472 - 1 5836 4215 5748 351 1533 255 cm:i:53 a152496f-c70a-4869-b7f7-2342f431585f_Basecall_1D_template 433 106 396 + 1 5836 2909 3222 131 313 255 cm:i:22 a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template 4456 335 4397 + 1 5836 1321 5257 1351 4062 255 cm:i:280 a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template 4456 3437 4349 + 1 5836 23 961 238 938 255 cm:i:40 a53eb8ee-85b3-4015-aeaa-00c7d69a359e_Basecall_1D_template 4456 86 537 + 1 5836 5334 5798 154 464 255 cm:i:26 b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template 4435 111 4359 - 1 5836 1673 5798 2062 4248 255 cm:i:487 b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template 4435 109 1619 - 1 5836 30 1525 472 1510 255 cm:i:68 bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template 4275 93 4048 + 1 5836 1733 5833 1303 4100 255 cm:i:230 bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template 4275 2532 4244 + 1 5836 4 1690 311 1712 255 cm:i:43 f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template 4509 289 4205 + 1 5836 23 3939 1039 3916 255 cm:i:166 f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template 4509 296 1782 + 1 5836 4242 5798 367 1556 255 cm:i:63 begin 5,836 5.33 0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template 4286 129 4010 + 1 6290 1009 5054 2431 4045 255 cm:i:529 0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template 4286 129 722 + 1 6290 5670 6287 297 617 255 cm:i:63 0237bf86-5cb0-4480-a66f-3eefdb9ef759_Basecall_1D_template 4286 3632 4010 + 1 6290 4 404 122 400 255 cm:i:19 054cd546-5f45-4edd-a9a4-b53d513cbc8c_Basecall_1D_template 4413 934 4391 - 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1 6265 1812 6233 2769 4421 255 cm:i:601 b9497173-8976-48fa-a822-93edea3f0baf_Basecall_1D_template 4435 105 1578 - 1 6265 74 1615 764 1541 255 cm:i:156 bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template 1421 122 847 + 1 6265 5182 5936 236 754 255 cm:i:36 bca7e454-f5a3-4320-b2bf-d50cd6cbfa2a_Basecall_1D_template 1421 149 847 + 1 6265 589 1322 155 733 255 cm:i:17 bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template 4275 124 4048 + 1 6265 1921 6262 2062 4341 255 cm:i:449 bd2c355e-c70e-42c7-a02f-810dd87fab35_Basecall_1D_template 4275 2532 4244 + 1 6265 4 1844 660 1840 255 cm:i:111 c2f682b3-3774-41a5-8663-32d081b558ee_Basecall_1D_template 1148 97 391 + 1 6265 2063 2361 157 298 255 cm:i:37 f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template 4509 289 4485 + 1 6265 23 4412 2182 4389 255 cm:i:436 f49ba5d3-abc3-4fc1-8efc-380b3238b0de_Basecall_1D_template 4509 111 1803 + 1 6265 4464 6248 787 1784 255 cm:i:141 3 6,265 8.04 Best polish: /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/racon_polish/016_rotated.fasta Saving /corral4/main/jobs/048/338/48338881/working/miniasm_assembly/13_racon_polished.gfa Assembly complete (2023-02-10 14:00:52) Saving /corral4/main/jobs/048/338/48338881/working/assembly.gfa ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 3, "fastq_input_selector": "none"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "10" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "21,23", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "0" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #5)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Output:** * ```console Starting Unicycler (2023-02-10 14:02:09) Welcome to Unicycler, an assembly pipeline for bacterial genomes. Since you provided only short reads, Unicycler will essentially function as a SPAdes- optimiser. It will try many k-mer sizes, choose the best based on contig length and graph connectivity, and scaffold the graph using SPAdes repeat resolution. For more information, please see https://github.com/rrwick/Unicycler Command: /usr/local/bin/unicycler -t 6 -o ./ --verbosity 3 -1 fq1.fastq -2 fq2.fastq --mode normal --min_fasta_length 100 --linear_seqs 0 --min_kmer_frac 0.2 --max_kmer_frac 0.95 --kmer_count 10 --depth_filter 0.25 --start_gene_id 90.0 --start_gene_cov 95.0 --min_component_size 1000 --min_dead_end_size 1000 --scores 3,-6,-5,-2 --keep 1 Unicycler version: v0.5.0 Using 6 threads The output directory already exists and files may be reused or overwritten: /corral4/main/jobs/048/338/48338893/working Bridging mode: normal using default normal bridge quality cutoff: 10.00 Dependencies: Program Version Status Path spades.py 3.15.5 good /usr/local/bin/spades.py racon not used makeblastdb 2.13.0+ good /usr/local/bin/makeblastdb tblastn 2.13.0+ good /usr/local/bin/tblastn Choosing k-mer range for assembly (2023-02-10 14:02:11) Unicycler chooses a k-mer range for SPAdes based on the length of the input reads. It uses a wide range of many k-mer sizes to maximise the chance of finding an ideal assembly. SPAdes maximum k-mer: 127 Median read length: 251 K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127 SPAdes assemblies (2023-02-10 14:02:12) Unicycler now uses SPAdes to assemble the short reads. It scores the assembly graph for each k-mer using the number of contigs (fewer is better) and the number of dead ends (fewer is better). The score function is 1/(c*(d+2)), where c is the contig count and d is the dead end count. spades.py -o /corral4/main/jobs/048/338/48338893/working/spades_assembly -k 27 --threads 6 --isolate -1 /corral4/main/jobs/048/338/48338893/working/fq1.fastq -2 /corral4/main/jobs/048/338/48338893/working/fq2.fastq -m 1024 == Warning == output dir is not empty! Please, clean output directory before run. Command: /usr/local/bin/spades.py -o /corral4/main/jobs/048/338/48338893/working/spades_assembly -k 27 --threads 6 --isolate -1 /corral4/main/jobs/048/338/48338893/working/fq1.fastq -2 /corral4/main/jobs/048/338/48338893/working/fq2.fastq -m 1024 System information: SPAdes version: 3.15.5 Python version: 3.8.13 OS: Linux-3.10.0-1062.18.1.el7.x86_64-x86_64-with-glibc2.10 Output dir: /corral4/main/jobs/048/338/48338893/working/spades_assembly Mode: ONLY assembling (without read error correction) Debug mode is turned OFF Dataset parameters: Isolate mode Reads: Library number: 1, library type: paired-end orientation: fr left reads: ['/corral4/main/jobs/048/338/48338893/working/fq1.fastq'] right reads: ['/corral4/main/jobs/048/338/48338893/working/fq2.fastq'] interlaced reads: not specified single reads: not specified merged reads: not specified Assembly parameters: k: [27] Repeat resolution is enabled Mismatch careful mode is turned OFF MismatchCorrector will be SKIPPED Coverage cutoff is turned OFF Other parameters: Dir for temp files: /corral4/main/jobs/048/338/48338893/working/spades_assembly/tmp Threads: 6 Memory limit (in Gb): 1024 ======= SPAdes pipeline started. Log can be found here: /corral4/main/jobs/048/338/48338893/working/spades_assembly/spades.log /corral4/main/jobs/048/338/48338893/working/fq1.fastq: max reads length: 251 /corral4/main/jobs/048/338/48338893/working/fq2.fastq: max reads length: 251 Reads length: 251 ===== Before start started. ===== Assembling started. ===== K27 started. == Running: /usr/local/bin/spades-core /corral4/main/jobs/048/338/48338893/working/spades_assembly/K27/configs/config.info /corral4/main/jobs/048/338/48338893/working/spades_assembly/K27/configs/isolate_mode.info 0:00:00.000 1M / 26M INFO General (main.cpp : 99) Loaded config from /corral4/main/jobs/048/338/48338893/working/spades_assembly/K27/configs/config.info 0:00:00.024 1M / 26M INFO General (main.cpp : 99) Loaded config from /corral4/main/jobs/048/338/48338893/working/spades_assembly/K27/configs/isolate_mode.info 0:00:00.036 1M / 26M INFO General (memory_limit.cpp : 54) Memory limit set to 1024 Gb 0:00:00.047 1M / 26M INFO General (main.cpp : 107) Starting SPAdes, built from N/A, git revision N/A 0:00:00.054 1M / 26M INFO General (main.cpp : 108) Maximum k-mer length: 128 0:00:00.062 1M / 26M INFO General (main.cpp : 109) Assembling dataset (/corral4/main/jobs/048/338/48338893/working/spades_assembly/dataset.info) with K=27 0:00:00.077 1M / 26M INFO General (main.cpp : 110) Maximum # of threads to use (adjusted due to OMP capabilities): 6 0:00:00.083 1M / 26M INFO General (pipeline.cpp : 212) SPAdes started 0:00:00.091 1M / 26M INFO General (pipeline.cpp : 225) Starting from stage: read_conversion 0:00:00.105 1M / 26M INFO General (pipeline.cpp : 231) Two-step repeat resolution disabled 0:00:00.115 1M / 26M INFO GraphCore (graph_core.hpp : 672) Graph created, vertex min_id: 3, edge min_id: 3 0:00:00.126 1M / 26M INFO GraphCore (graph_core.hpp : 673) Vertex size: 48, edge size: 40 0:00:00.136 1M / 26M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:00.149 1M / 26M INFO General (pipeline.cpp : 242) Will need read mapping, kmer mapper will be attached 0:00:00.160 1M / 26M INFO StageManager (stage.cpp : 185) STAGE == Binary Read Conversion (id: read_conversion) 0:00:00.170 1M / 26M INFO General (read_converter.cpp : 72) Converting reads to binary format for library #0 (takes a while) 0:00:00.175 1M / 26M INFO General (read_converter.cpp : 73) Converting paired reads 0:00:00.257 63M / 63M INFO General (binary_converter.cpp : 111) 7925 reads written 0:00:00.270 41M / 41M INFO General (read_converter.cpp : 86) Converting single reads 0:00:00.334 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.347 41M / 41M INFO General (read_converter.cpp : 92) Converting merged reads 0:00:00.382 51M / 51M INFO General (binary_converter.cpp : 111) 0 reads written 0:00:00.448 1M / 26M INFO StageManager (stage.cpp : 185) STAGE == de Bruijn graph construction (id: construction) 0:00:00.474 1M / 26M INFO General (construction.cpp : 153) Max read length 251 0:00:00.484 1M / 26M INFO General (construction.cpp : 159) Average read length 250.525 0:00:00.493 1M / 26M INFO General (stage.cpp : 117) PROCEDURE == k+1-mer counting (id: construction:kpomer_counting) 0:00:00.502 1M / 26M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 60 files using 6 threads. This might take a while. 0:00:00.553 1M / 26M INFO General (file_limit.hpp : 42) Open file limit set to 131072 0:00:00.571 1M / 26M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 56.8889 Gb 0:00:00.587 1M / 26M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118481 0:00:01.075 1M / 65M INFO General (kmer_splitters.hpp : 131) Used 31700 reads 0:00:01.095 1M / 65M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:01.308 1M / 65M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 35249 kmers in total. 0:00:01.313 1M / 65M INFO General (stage.cpp : 117) PROCEDURE == Extension index construction (id: construction:extension_index_construction) 0:00:01.362 1M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 438) Building kmer index 0:00:01.365 1M / 65M INFO General (kmer_index_builder.hpp : 243) Splitting kmer instances into 60 files using 6 threads. This might take a while. 0:00:01.376 1M / 65M INFO General (file_limit.hpp : 42) Open file limit set to 131072 0:00:01.385 1M / 65M INFO General (kmer_splitter.hpp : 93) Memory available for splitting buffers: 56.8889 Gb 0:00:01.395 1M / 65M INFO General (kmer_splitter.hpp : 101) Using cell size of 1118481 0:00:01.752 3601M / 3601M INFO General (kmer_splitters.hpp : 194) Processed 35249 kmers 0:00:01.763 3601M / 3601M INFO General (kmer_splitters.hpp : 199) Used 35249 kmers. 0:00:01.773 1M / 65M INFO General (kmer_index_builder.hpp : 249) Starting k-mer counting. 0:00:02.059 1M / 65M INFO General (kmer_index_builder.hpp : 260) K-mer counting done. There are 34510 kmers in total. 0:00:02.069 1M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:02.108 1M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 34510 kmers, 71424 bytes occupied (16.5573 bits per kmer). 0:00:02.114 1M / 65M INFO General (kmer_index_builder.hpp : 169) Merging final buckets. 0:00:02.324 1M / 65M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 100) Building k-mer extensions from k+1-mers 0:00:02.363 1M / 65M INFO DeBruijnExtensionIndexBu (kmer_extension_index_build: 105) Building k-mer extensions from k+1-mers finished. 0:00:02.373 1M / 65M INFO General (stage.cpp : 117) PROCEDURE == Condensing graph (id: construction:graph_condensing) 0:00:02.409 1M / 65M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 354) Extracting unbranching paths 0:00:02.425 1M / 65M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 373) Extracting unbranching paths finished. 2775 sequences extracted 0:00:02.435 1M / 65M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 309) Collecting perfect loops 0:00:02.445 1M / 65M INFO UnbranchingPathExtractor (debruijn_graph_constructor: 342) Collecting perfect loops finished. 0 loops collected 0:00:02.450 1M / 65M INFO General (debruijn_graph_constructor: 487) Total 5550 edges to create 0:00:02.453 1M / 65M INFO General (debruijn_graph_constructor: 489) Collecting link records 0:00:02.462 1M / 65M INFO General (debruijn_graph_constructor: 491) Ordering link records 0:00:02.473 1M / 65M INFO General (debruijn_graph_constructor: 493) Sorting done 0:00:02.473 1M / 65M INFO General (debruijn_graph_constructor: 503) Total 2036 vertices to create 0:00:02.474 2M / 65M INFO General (debruijn_graph_constructor: 506) Connecting the graph 0:00:02.476 1M / 65M INFO General (stage.cpp : 117) PROCEDURE == Filling coverage indices (PHM) (id: construction:coverage_filling_phm) 0:00:02.476 1M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:02.495 2M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 35249 kmers, 71912 bytes occupied (16.3209 bits per kmer). 0:00:02.496 2M / 65M INFO General (coverage_hash_map_builder.: 47) Collecting k-mer coverage information from reads, this takes a while. 0:00:02.616 2M / 65M INFO General (construction.cpp : 430) Filling coverage and flanking coverage from PHM 0:00:02.619 2M / 65M INFO General (coverage_filling.hpp : 82) Processed 5550 edges 0:00:02.686 1M / 65M INFO StageManager (stage.cpp : 185) STAGE == EC Threshold Finding (id: ec_threshold_finder) 0:00:02.689 1M / 65M INFO General (kmer_coverage_model.cpp : 181) Kmer coverage valley at: 7 0:00:02.693 1M / 65M INFO General (kmer_coverage_model.cpp : 201) K-mer histogram maximum: 695 0:00:02.699 1M / 65M INFO General (kmer_coverage_model.cpp : 237) Estimated median coverage: 695. Coverage mad: 91.9212 0:00:02.709 1M / 65M INFO General (kmer_coverage_model.cpp : 259) Fitting coverage model 0:00:02.879 1M / 65M INFO General (kmer_coverage_model.cpp : 295) ... iteration 2 0:00:03.150 1M / 65M INFO General (kmer_coverage_model.cpp : 295) ... iteration 4 0:00:03.800 1M / 65M INFO General (kmer_coverage_model.cpp : 295) ... iteration 8 0:00:04.597 1M / 65M INFO General (kmer_coverage_model.cpp : 295) ... iteration 16 0:00:05.968 1M / 65M INFO General (kmer_coverage_model.cpp : 295) ... iteration 32 0:00:05.970 1M / 65M INFO General (kmer_coverage_model.cpp : 309) Fitted mean coverage: 671.577. Fitted coverage std. dev: 114.418 0:00:05.977 1M / 65M INFO General (kmer_coverage_model.cpp : 334) Probability of erroneous kmer at valley: 1 0:00:05.982 1M / 65M INFO General (kmer_coverage_model.cpp : 358) Preliminary threshold calculated as: 275 0:00:05.986 1M / 65M INFO General (kmer_coverage_model.cpp : 362) Threshold adjusted to: 275 0:00:05.991 1M / 65M INFO General (kmer_coverage_model.cpp : 375) Estimated genome size (ignoring repeats): 5132 0:00:05.995 1M / 65M INFO General (genomic_info_filler.cpp : 55) Mean coverage was calculated as 671.577 0:00:06.000 1M / 65M INFO General (genomic_info_filler.cpp : 70) EC coverage threshold value was calculated as 275 0:00:06.004 1M / 65M INFO General (genomic_info_filler.cpp : 71) Trusted kmer low bound: 0 0:00:06.009 1M / 65M INFO StageManager (stage.cpp : 185) STAGE == Gap Closer (id: early_gapcloser) 0:00:06.024 10M / 65M INFO General (edge_index.hpp : 113) Size of edge index entries: 12/8 0:00:06.033 10M / 65M INFO General (gap_closer.cpp : 101) Total edges in tip neighborhood: 415 out of 5550, length: 7516 0:00:06.039 10M / 65M INFO General (edge_index.hpp : 167) Using small index (max_id = 5580) 0:00:06.049 10M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 395) Building perfect hash indices 0:00:06.169 10M / 65M INFO K-mer Index Building (kmer_index_builder.hpp : 431) Index built. Total 7516 kmer .. bs/048/338/48338893/working/spades_assembly/K127/assembly_graph.fastg 0:00:06.708 3M / 128M INFO General (contig_output_stage.cpp : 196) Breaking scaffolds 0:00:06.708 3M / 128M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/final_contigs.fasta 0:00:06.711 3M / 128M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/final_contigs.paths 0:00:06.713 3M / 128M INFO General (contig_output_stage.cpp : 98) Outputting contigs to /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/scaffolds.fasta 0:00:06.715 3M / 128M INFO General (contig_output_stage.cpp : 104) Outputting FastG paths to /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/scaffolds.paths 0:00:06.747 3M / 128M INFO General (contig_output_stage.cpp : 111) Populating GFA with scaffold paths 0:00:06.760 3M / 128M INFO General (pipeline.cpp : 287) SPAdes finished 0:00:06.774 1M / 128M INFO General (main.cpp : 136) Assembling time: 0 hours 0 minutes 6 seconds ===== K127 finished. ===== Copy files started. == Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/copy_files.py /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/before_rr.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/before_rr.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/assembly_graph_after_simplification.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/assembly_graph_after_simplification.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/final_contigs.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/contigs.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/first_pe_contigs.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/first_pe_contigs.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/strain_graph.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/strain_graph.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/scaffolds.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/scaffolds.fasta /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/scaffolds.paths /corral4/main/jobs/048/338/48338893/working/spades_assembly/scaffolds.paths /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/assembly_graph_with_scaffolds.gfa /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/assembly_graph.fastg /corral4/main/jobs/048/338/48338893/working/spades_assembly/assembly_graph.fastg /corral4/main/jobs/048/338/48338893/working/spades_assembly/K127/final_contigs.paths /corral4/main/jobs/048/338/48338893/working/spades_assembly/contigs.paths ===== Copy files finished. ===== Assembling finished. ===== Breaking scaffolds started. == Running: /usr/local/bin/python /usr/local/share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py --result_scaffolds_filename /corral4/main/jobs/048/338/48338893/working/spades_assembly/scaffolds.fasta --misc_dir /corral4/main/jobs/048/338/48338893/working/spades_assembly/misc --threshold_for_breaking_scaffolds 3 ===== Breaking scaffolds finished. ===== Terminate started. ===== Terminate finished. * Assembled contigs are in /corral4/main/jobs/048/338/48338893/working/spades_assembly/contigs.fasta * Assembled scaffolds are in /corral4/main/jobs/048/338/48338893/working/spades_assembly/scaffolds.fasta * Paths in the assembly graph corresponding to the contigs are in /corral4/main/jobs/048/338/48338893/working/spades_assembly/contigs.paths * Paths in the assembly graph corresponding to the scaffolds are in /corral4/main/jobs/048/338/48338893/working/spades_assembly/scaffolds.paths * Assembly graph is in /corral4/main/jobs/048/338/48338893/working/spades_assembly/assembly_graph.fastg * Assembly graph in GFA format is in /corral4/main/jobs/048/338/48338893/working/spades_assembly/assembly_graph_with_scaffolds.gfa ======= SPAdes pipeline finished. SPAdes log can be found here: /corral4/main/jobs/048/338/48338893/working/spades_assembly/spades.log Thank you for using SPAdes! Insert size mean: 367.3 bp Insert size stdev: 37.3 bp Cleaning k27 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k027_assembly_graph.gfa Cleaning k47 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k047_assembly_graph.gfa Cleaning k63 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k063_assembly_graph.gfa Cleaning k77 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k077_assembly_graph.gfa Cleaning k89 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k089_assembly_graph.gfa Cleaning k99 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k099_assembly_graph.gfa Cleaning k107 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k107_assembly_graph.gfa Cleaning k115 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k115_assembly_graph.gfa Cleaning k121 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k121_assembly_graph.gfa Cleaning k127 graph Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k127_assembly_graph.gfa Repair multi way junctions (2023-02-10 14:05:10) Filter by read depth (2023-02-10 14:05:10) Filter homopolymer loops (2023-02-10 14:05:10) Merge all possible (2023-02-10 14:05:10) Normalise read depths (2023-02-10 14:05:10) Remove zero length segments (2023-02-10 14:05:10) Sort link order (2023-02-10 14:05:10) Graph cleaning finished (2023-02-10 14:05:10) Saving /corral4/main/jobs/048/338/48338893/working/spades_assembly/k27_assembly_graph.gfa SPAdes assembly graph summary (2023-02-10 14:05:10) K-mer Contigs Links Total length N50 Longest contig Dead ends Score 27 1 1 5,413 5,413 5,413 0 5.00e-01 <-best 47 1 1 5,433 5,433 5,433 0 5.00e-01 63 1 1 5,449 5,449 5,449 0 5.00e-01 77 1 1 5,463 5,463 5,463 0 5.00e-01 89 1 1 5,475 5,475 5,475 0 5.00e-01 99 1 1 5,485 5,485 5,485 0 5.00e-01 107 1 1 5,493 5,493 5,493 0 5.00e-01 115 1 1 5,501 5,501 5,501 0 5.00e-01 121 1 1 5,507 5,507 5,507 0 5.00e-01 127 1 1 5,513 5,513 5,513 0 5.00e-01 Read depth filter: removed 0 contigs totalling 0 bp Deleting /corral4/main/jobs/048/338/48338893/working/spades_assembly/ Determining graph multiplicity (2023-02-10 14:05:10) Multiplicity is the number of times a sequence occurs in the underlying sequence. Single-copy contigs (those with a multiplicity of one, occurring only once in the underlying sequence) are particularly useful. Multiplicity determination begins by identifying contigs which are clearly single-copy because they are of low depth and do not have more than one link per side. Median depth of 10 longest contigs: 1.00 Initial single copy segments: 1 Unicycler now uses a greedy algorithm to propagate multiplicity through the graph. For example, if two single-copy contigs merge together, the resulting contig will get a multiplicity of two. When no more propagation is possible, additional single-copy contigs are added and the process is repeated. This allows for multiplicity to be correctly assigned to the chromosome (at the median depth) but also for plasmids (which may be higher or lower in depth). MERGING MULTIPLICITY SPLITTING MULTIPLICITY FINDING NEW SINGLE-COPY MERGING MULTIPLICITY SPLITTING MULTIPLICITY REMOVING PROPAGATION TOLERANCE MERGING MULTIPLICITY SPLITTING MULTIPLICITY Saving /corral4/main/jobs/048/338/48338893/working/002_depth_filter.gfa Cleaning graph (2023-02-10 14:05:10) Unicycler now performs various cleaning procedures on the graph to remove overlaps and simplify the graph structure. The end result is a graph ready for bridging. Grouping graph edges based on overlap removal 0 / 2 (0.0%) 1 / 2 (50.0%) 2 / 2 (100.0%) Removing graph overlaps Bases Bases trimmed trimmed Segment from from number start end 1 13 14 Graph overlaps removed Saving /corral4/main/jobs/048/338/48338893/working/003_overlaps_removed.gfa Unicycler now selects a set of anchor contigs from the single-copy contigs. These are the contigs which will be connected via bridges to form the final assembly. 1 anchor segments (5,386 bp) out of 1 total segments (5,386 bp) Anchor segments: 1 Creating SPAdes contig bridges (2023-02-10 14:05:10) SPAdes uses paired-end information to perform repeat resolution (RR) and produce contigs from the assembly graph. SPAdes saves the graph paths corresponding to these contigs in the contigs.paths file. When one of these paths contains two or more anchor contigs, Unicycler can create a bridge from the path. No SPAdes contig bridges Creating loop unrolling bridges (2023-02-10 14:05:10) When a SPAdes contig path connects an anchor contig with the middle contig of a simple loop, Unicycler concludes that the sequences are contiguous (i.e. the loop is not a separate piece of DNA). It then uses the read depth of the middle and repeat contigs to guess the number of times to traverse the loop and makes a bridge. No loop unrolling bridges made none found Applying bridges (2023-02-10 14:05:10) Unicycler now applies to the graph in decreasing order of quality. This ensures that when multiple, contradictory bridges exist, the most supported option is used. Bridge type Start -> end Path Quality Result Saving /corral4/main/jobs/048/338/48338893/working/004_bridges_applied.gfa Cleaning up leftover segments (2023-02-10 14:05:10) Segments eligible for deletion: Bridged assembly graph (2023-02-10 14:05:10) The assembly is now mostly finished and no more structural changes will be made. Ideally the assembly graph should now have one contig per replicon and no erroneous contigs (i.e. a complete assembly). If there are more contigs, then the assembly is not complete. Saving /corral4/main/jobs/048/338/48338893/working/005_final_clean.gfa Component Segments Links Length N50 Longest segment Status 1 1 1 5,386 5,386 5,386 complete Rotating completed replicons (2023-02-10 14:05:10) Any completed circular contigs (i.e. single contigs which have one link connecting end to start) can have their start position changed without altering the sequence. For consistency, Unicycler now searches for a starting gene (dnaA or repA) in each such contig, and if one is found, the contig is rotated to start with that gene on the forward strand. Segment 1: makeblastdb -dbtype nucl -in replicon.fasta tblastn -db replicon.fasta -query /usr/local/lib/python3.8/site-packages/unicycler/gene_data/start_genes.fasta -outfmt 6 qseqid sstart send pident qlen qseq qstart bitscore -num_threads 1 Segment Length Depth Starting gene Position Strand Identity Coverage 1 5,386 1.00x none found Assembly complete (2023-02-10 14:05:25) Saving /corral4/main/jobs/048/338/48338893/working/assembly.gfa Saving /corral4/main/jobs/048/338/48338893/working/assembly.fasta ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108184204, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108184210, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | long | ` None ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "1" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |
✅ toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler (Test #6)
**Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Traceback:** * ```console ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | paired\_unpaired | ` {"__current_case__": 0, "fastq_input1": {"values": [{"id": 108184204, "src": "hda"}]}, "fastq_input2": {"values": [{"id": 108184210, "src": "hda"}]}, "fastq_input_selector": "paired"} ` | | mode | ` "normal" ` | | min\_fasta\_length | ` "100" ` | | linear\_seqs | ` "0" ` | | min\_anchor\_seg\_len | ` "" ` | | spades | ` {"depth_filter": "0.25", "kmer_count": "10", "kmers": "", "largest_component": false, "max_kmer_frac": "0.95", "min_kmer_frac": "0.2"} ` | | rotation | ` {"no_rotate": false, "start_gene_cov": "95.0", "start_gene_id": "90.0", "start_genes": null} ` | | graph\_clean | ` {"min_component_size": "1000", "min_dead_end_size": "1000"} ` | | lr\_align | ` {"contamination": null, "low_score": "", "no_simple_bridges": false, "scores": "3,-6,-5,-2"} ` | | keep | ` "2" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

jennaj commented 1 year ago

Fixed 👍

mvdbeek / usegalaxy-tests

test unicycler 0.5.0+galaxy1 #74

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