Test trinotate 3.2.2+galaxy0

[natefoo]

Installed in galaxyproject/usegalaxy-tools#448

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	2
Passed	0
Error	1
Failure	1
Skipped	0

Errored s

*

❌ toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate (Test #2)

**Execution Problem:** * ``` Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: . ```

Failed s

*

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

**Problems**: * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found . ``` * ``` Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0, exit_code: 127, stderr: /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 127 ``` **Standard Error:** * ```console /corral4/main/jobs/039/504/39504519/tool_script.sh: line 9: Build_Trinotate_Boilerplate_SQLite_db.pl: not found ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | cond\_download | ` {"__current_case__": 1, "select_download": "yes"} ` | | report\_option | ` {"E": "1e-05", "incl_pep": "false", "incl_trans": "false", "pfam_cutoff": "DNC"} ` | | keep\_sqlite | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

[natefoo]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0

Might fail due to output size differences but the tool should run now. Here's what I got locally:

Expected file size was 573911, actual file size was 573236 (difference of 100 accepted)

[mvdbeek]

Results (powered by Planemo)

Summary

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

Failed s

*

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

**Problems**: * ``` Output trinotate_out: different than expected, difference (using diff): ( /tmp/tmpv_iw52ritrinotate_annotation_report.xls v. /tmp/tmp587viv5wtrinotate_annotation_report.xls ) --- local_file +++ history_data @@ -6,9 +6,9 @@ TRINITY_DN594_c0_g2 TRINITY_DN594_c0_g2_i1 ERG27_SCHPO^ERG27_SCHPO^Q:1207-680,H:46-205^90.91%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces`ERG27_SCHPO^ERG27_SCHPO^Q:681-349,H:228-338^100%ID^E:2e-141^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN594_c0_g2_i1|m.613 653-1207[-] ERG27_SCHPO^ERG27_SCHPO^Q:1-176,H:46-205^90.91%ID^E:2e-108^RecName: Full=3-keto-steroid reductase;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPBC1709.07 GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0005811^cellular_component^lipid droplet`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process GO:0005789^cellular_component^endoplasmic reticulum membrane`GO:0005811^cellular_component^lipid droplet`GO:0000253^molecular_function^3-keto sterol reductase activity`GO:0006696^biological_process^ergosterol biosynthetic process . . . TRINITY_DN591_c0_g1 TRINITY_DN591_c0_g1_i1 SYNM_SCHPO^SYNM_SCHPO^Q:1742-738,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN591_c0_g1_i1|m.617 735-1742[-] SYNM_SCHPO^SYNM_SCHPO^Q:1-335,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPBC1198.10c GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation . . . TRINITY_DN591_c0_g1 TRINITY_DN591_c0_g1_i1 SYNM_SCHPO^SYNM_SCHPO^Q:1742-738,H:107-441^100%ID^E:0^RecName: Full=Asparagine--tRNA ligase, mitochondrial;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN591_c0_g1_i1|m.618 251-733[+] UBC16_SCHPO^UBC16_SCHPO^Q:1-160,H:1-160^100%ID^E:2e-116^RecName: Full=Ubiquitin-conjugating enzyme E2 16;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPBC1198.09 GO:0005759^cellular_component^mitochondrial matrix`GO:0005739^cellular_component^mitochondrion`GO:0004816^molecular_function^asparagine-tRNA ligase activity`GO:0005524^molecular_function^ATP binding`GO:0000049^molecular_function^tRNA binding`GO:0006421^biological_process^asparaginyl-tRNA aminoacylation`GO:0032543^biological_process^mitochondrial translation GO:0005634^cellular_component^nucleus`GO:0005524^molecular_function^ATP binding`GO:0061631^molecular_function^ubiquitin conjugating enzyme activity`GO:0007031^biological_process^peroxisome organization`GO:0070647^biological_process^protein modification by small protein conjugation or removal`GO:0000209^biological_process^protein polyubiquitination . . . -TRINITY_DN540_c0_g1 TRINITY_DN540_c0_g1_i1 PPZ_SCHPO^PPZ_SCHPO^Q:26-1567,H:2-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g1_i1|m.650 350-1570[+] PPZ_SCHPO^PPZ_SCHPO^Q:1-406,H:110-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . -TRINITY_DN540_c0_g2 TRINITY_DN540_c0_g2_i1 PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g2_i1|m.651 300-1847[+] PPZ_SCHPO^PPZ_SCHPO^Q:1-515,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . -TRINITY_DN540_c0_g2 TRINITY_DN540_c0_g2_i1 PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g2_i1|m.652 1-393[+] . . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0106306^molecular_function^protein serine phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0106307^molecular_function^protein threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . . +TRINITY_DN540_c0_g1 TRINITY_DN540_c0_g1_i1 PPZ_SCHPO^PPZ_SCHPO^Q:26-1567,H:2-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g1_i1|m.650 350-1570[+] PPZ_SCHPO^PPZ_SCHPO^Q:1-406,H:110-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . +TRINITY_DN540_c0_g2 TRINITY_DN540_c0_g2_i1 PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g2_i1|m.651 300-1847[+] PPZ_SCHPO^PPZ_SCHPO^Q:1-515,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . +TRINITY_DN540_c0_g2 TRINITY_DN540_c0_g2_i1 PPZ_SCHPO^PPZ_SCHPO^Q:300-1844,H:1-515^100%ID^E:0^RecName: Full=Serine/threonine-protein phosphatase PP-Z;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN540_c0_g2_i1|m.652 1-393[+] . . . . . KEGG:spo:SPAC57A7.08 GO:0005737^cellular_component^cytoplasm`GO:0005783^cellular_component^endoplasmic reticulum`GO:0000324^cellular_component^fungal-type vacuole`GO:0005634^cellular_component^nucleus`GO:0046872^molecular_function^metal ion binding`GO:0016791^molecular_function^phosphatase activity`GO:0004722^molecular_function^protein serine/threonine phosphatase activity`GO:0007165^biological_process^signal transduction . . . . TRINITY_DN597_c0_g1 TRINITY_DN597_c0_g1_i1 KAPR_SCHPO^KAPR_SCHPO^Q:202-1437,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN597_c0_g1_i1|m.662 202-1440[+] KAPR_SCHPO^KAPR_SCHPO^Q:1-412,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC8C9.03 GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling . . . TRINITY_DN597_c0_g2 TRINITY_DN597_c0_g2_i1 KAPR_SCHPO^KAPR_SCHPO^Q:202-1437,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . TRINITY_DN597_c0_g2_i1|m.663 202-1440[+] KAPR_SCHPO^KAPR_SCHPO^Q:1-412,H:1-412^100%ID^E:0^RecName: Full=cAMP-dependent protein kinase regulatory subunit;^Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina; Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae; Schizosaccharomyces . . . . KEGG:spo:SPAC8C9.03 GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling GO:0005952^cellular_component^cAMP-dependent protein kinase complex`GO:0005737^cellular_component^cytoplasm`GO:0005829^cellular_component^cytosol`GO:0005634^cellular_component^nucleus`GO:0030552^molecular_function^cAMP binding`GO:0004862^molecular_function^cAMP-dependent protein kinase inhibitor activity`GO:0008603^molecular_function^cAMP-dependent protein kinase regulator activity`GO:0007189^biological_process^adenylate cyclase-activating G protein-coupled receptor signaling pathway`GO:0042149^biological_process^cellular response to glucose starvation`GO:0110034^biological_process^negative regulation of adenylate cyclase-activating glucose-activated G protein-coupled receptor signaling pathway`GO:0046827^biological_process^positive regulation of protein export from nucleus`GO:0043949^biological_process^regulation of cAMP-mediated signaling`GO:0010738^biological_process^regulation of protein kinase A signaling . . . TRINITY_DN547_c0_g1 TRINITY_DN547_c0_g1_i1 . . . . . . . . . . . . . . . ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console * Running CMD: wget "http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" --2021-12-21 13:41:26-- http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74 Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 625798251 (597M) [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' 0K .......... .......... .......... .......... .......... 0% 3.39K 2d2h 50K .......... .......... .......... .......... .......... 0% 417K 25h15m 100K ... 0% 23.5M=15s 2021-12-21 13:41:42 (6.94 KB/s) - Connection closed at byte 105788. Retrying. --2021-12-21 13:41:43-- (try: 2) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 625692463 (597M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 100K ] 100K ,,,....... .......... .......... .......... .......... 0% 7.90K 23h1m 150K .......... .......... .......... .......... .......... 0% 12.8K 17h58m 200K .......... .......... .......... .......... .......... 0% 437K 11h58m 250K .......... .......... .......... .......... .......... 0% 417K 9h2m 300K .......... .......... .......... .......... .......... 0% 14.0M 7h12m 350K .......... .......... .......... .......... .......... 0% 372K 6h4m 400K .......... .......... .......... .......... .......... 0% 474K 5h14m 450K .......... .......... .......... .......... .......... 0% 418K 4h38m 500K .......... .......... .......... .......... .......... 0% 1.27M 4h7m 550K .......... .......... .......... .......... .......... 0% 351K 3h45m 600K .......... .......... .......... .......... .......... 0% 27.8K 3h58m 650K .......... .......... .......... .......... .......... 0% 24.0K 4h14m 700K .......... .......... .......... .......... .......... 0% 415K 3h56m 750K .......... .......... .......... .......... .......... 0% 609K 3h40m 800K .......... .......... .......... .......... .......... 0% 675K 3h26m 850K .......... .......... .......... .......... .......... 0% 591K 3h14m 900K .......... .......... .......... .......... .......... 0% 418K 3h4m 950K .......... .......... .......... .......... .......... 0% 682K 2h55m 1000K .......... .......... .......... .......... .......... 0% 424K 2h47m 1050K .......... .......... .......... .......... .......... 0% 413K 2h40m 1100K .......... .......... .......... .......... .......... 0% 22.5K 2h54m 1150K .......... .......... .......... .......... .......... 0% 11.6K 3h25m 1200K .......... .......... .......... .......... .......... 0% 6.47M 3h17m 1250K .......... .......... .......... .......... .......... 0% 411K 3h9m 1300K .......... .......... .......... .......... .......... 0% 418K 3h3m 1350K .......... .......... .......... .......... .......... 0% 448K 2h56m 1400K .......... .......... .......... .......... .......... 0% 416K 2h51m 1450K .......... .......... .......... .......... .......... 0% 1.03M 2h45m 1500K .......... .......... .......... .......... .......... 0% 415K 2h40m 1550K .......... .......... .......... .......... .......... 0% 598K 2h35m 1600K .......... .......... .......... .......... .......... 0% 9.27K 3h6m 1650K .......... .......... .......... .......... .......... 0% 159M 3h0m 1700K .......... .......... .......... .......... .......... 0% 5.49K 3h50m 1750K .......... .......... .......... .......... .......... 0% 417K 3h44m 1800K .......... .......... .......... .......... .......... 0% 417K 3h39m 1850K .......... .......... .......... .......... .......... 0% 417K 3h33m 1900K .......... .......... .......... .......... .......... 0% 62.5M 3h27m 1950K .......... .......... .......... .......... .......... 0% 416K 3h23m 2000K .......... .......... .......... .......... .......... 0% 418K 3h18m 2050K .......... .......... .......... .......... .......... 0% 417K 3h14m 2100K .......... .......... .......... .......... .......... 0% 638K 3h9m 2150K .......... .......... .......... .... 0% 2.49K=52s 2021-12-21 13:42:36 (39.9 KB/s) - Connection closed at byte 2236960. Retrying. --2021-12-21 13:42:38-- (try: 3) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 623561291 (595M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 2150K ] 2150K ,,,,,,,,,, ,,,,,,,,,, ,,,,,,,,,, ,,,,...... .......... 0% 5.86K 3d21h 2200K .......... .......... .......... .......... .......... 0% 539K 22h17m 2250K .......... .......... .......... .......... .......... 0% 6.03K 24h47m 2300K .......... .......... .......... .......... .......... 0% 695K 17h22m 2350K .......... .......... .......... .......... .......... 0% 416K 13h26m 2400K .......... .......... .......... .......... .......... 0% 417K 10h58m 2450K .......... .......... .......... .......... .......... 0% 86.1M 9h14m 2500K .......... .......... .......... .......... .......... 0% 291K 8h3m 2550K .......... .......... .......... .......... .......... 0% 5.58K 10h43m 2600K .......... .......... .......... .......... .......... 0% 938K 9h35m 2650K .......... .......... .......... .......... .......... 0% 637K 8h41m 2700K .......... .......... .......... .......... .......... 0% 413K 7h57m 2750K .......... .......... .......... .......... .......... 0% 5.34K 9h52m 2800K .......... .......... .......... .......... .......... 0% 549K 9h9m 2850K .......... .......... .......... .......... .......... 0% 416K 8h32m 2900K .......... .......... .......... .......... .......... 0% 1.64M 7h59m 2950K .......... .......... .......... .......... .......... 0% 415K 7h31m 3000K .......... .......... .......... .......... .......... 0% 417K 7h7m 3050K .......... .......... .......... .......... .......... 0% 547K 6h44m 3100K .......... .......... .......... .......... .......... 0% 5.13K 8h6m 3150K .......... .......... .......... .......... .......... 0% 200K 7h44m 3200K .......... .......... .......... .......... .......... 0% 217M 7h22m 3250K .......... .......... .......... .......... .......... 0% 4.06K 8h54m 3300K .......... .......... .......... .......... ....... 0% 335K=59s 2021-12-21 13:43:37 (19.7 KB/s) - Connection closed at byte 3428120. Retrying. --2021-12-21 13:43:40-- (try: 4) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 622370131 (594M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 3300K ] 3300K ,,,,,,,,,, ,,,,,,,,,, ,,,,,,,,,, ,,,,,,,,,, ,,,,,,,... 0% 2.31G 6s 3350K .......... .......... .......... .......... .......... 0% 243K 39m51s 3400K .......... .......... .......... .......... .......... 0% 416K 32m15s 3450K .......... .......... .......... .......... .......... 0% 416K 29m39s 3500K .......... .......... .......... .......... .......... 0% 160M 22m20s 3550K .......... .......... .......... .......... .......... 0% 416K 22m44s 3600K .......... .......... .......... .......... .......... 0% 417K 22m59s 3650K .......... .......... .......... .......... .......... 0% 417K 23m10s 3700K .......... .......... .......... .......... .......... 0% 417K 23m18s 3750K .......... .......... .......... .......... .......... 0% 77.5M 20m44s 3800K .......... .......... .......... .......... 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.......... .......... .......... .......... .......... 99% 201M 0s 284800K .......... .......... .......... .......... .......... 99% 51.8M 0s 284850K .......... .......... .......... .......... .......... 99% 261M 0s 284900K .......... .......... .......... .......... .......... 99% 263M 0s 284950K .......... .......... .......... .......... .......... 99% 253M 0s 285000K .......... .......... .......... .......... .......... 99% 50.7M 0s 285050K .......... .......... .......... .......... .......... 99% 275M 0s 285100K .......... .......... .......... .......... .......... 99% 277M 0s 285150K .......... .......... .......... .......... .......... 99% 62.8M 0s 285200K .......... .......... .......... .......... .......... 99% 248M 0s 285250K .......... .......... .......... .......... .......... 99% 253M 0s 285300K .......... .......... .......... .......... .......... 99% 262M 0s 285350K .......... .......... .......... .......... .......... 99% 12.0M 0s 285400K .......... .......... .......... .......... .......... 99% 2.12M 0s 285450K .......... .......... .......... .......... .......... 99% 247M 0s 285500K .......... .......... .......... .......... .......... 99% 259M 0s 285550K .......... .......... .......... .......... .......... 99% 261M 0s 285600K .......... .......... .......... .......... .......... 99% 207M 0s 285650K .......... .......... .......... .......... .......... 99% 275M 0s 285700K .......... .......... .......... .......... .......... 99% 54.1M 0s 285750K .......... .......... .......... .......... .......... 99% 13.3M 0s 285800K .......... .......... .......... .......... .......... 99% 166M 0s 285850K .......... .......... .......... .......... .......... 99% 60.7M 0s 285900K .......... .......... .......... .......... .......... 99% 186M 0s 285950K .......... .......... .......... .......... .......... 99% 83.1M 0s 286000K .......... .......... .......... .......... .......... 99% 170M 0s 286050K .......... .......... .......... .......... .......... 99% 8.26M 0s 286100K .......... .......... .......... ... 100% 237M=14s 2021-12-21 14:10:28 (20.3 MB/s) - 'Pfam-A.hmm.gz' saved [293000230] * Running CMD: /usr/local/bin/PFAM_dat_parser.pl Pfam-A.hmm.gz [100] [200] [300] [400] [500] [600] [700] [800] [900] [1000] [1100] [1200] [1300] [1400] [1500] [1600] [1700] [1800] [1900] [2000] [2100] [2200] [2300] [2400] [2500] [2600] [2700] [2800] [2900] [3000] [3100] [3200] [3300] [3400] [3500] [3600] [3700] [3800] [3900] [4000] [4100] [4200] [4300] [4400] [4500] [4600] [4700] [4800] [4900] [5000] [5100] [5200] [5300] [5400] [5500] [5600] [5700] [5800] [5900] [6000] [6100] [6200] [6300] [6400] [6500] [6600] [6700] [6800] [6900] [7000] [7100] [7200] [7300] [7400] [7500] [7600] [7700] [7800] [7900] [8000] [8100] [8200] [8300] [8400] [8500] [8600] [8700] [8800] [8900] [9000] [9100] [9200] [9300] [9400] [9500] [9600] [9700] [9800] [9900] [10000] [10100] [10200] [10300] [10400] [10500] [10600] [10700] [10800] [10900] [11000] [11100] [11200] [11300] [11400] [11500] [11600] [11700] [11800] [11900] [12000] [12100] [12200] [12300] [12400] [12500] [12600] [12700] [12800] [12900] [13000] [13100] [13200] [13300] [13400] [13500] [13600] [13700] [13800] [13900] [14000] [14100] [14200] [14300] [14400] [14500] [14600] [14700] [14800] [14900] [15000] [15100] [15200] [15300] [15400] [15500] [15600] [15700] [15800] [15900] [16000] [16100] [16200] [16300] [16400] [16500] [16600] [16700] [16800] [16900] [17000] [17100] [17200] [17300] [17400] [17500] [17600] [17700] [17800] [17900] [18000] [18100] [18200] [18300] [18400] [18500] [18600] [18700] [18800] [18900] [19000] [19100] [19200] [19300] [19400] [19500] [19600] * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam Pfam-A.hmm.gz.pfam_sqlite_bulk_load CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import Pfam-A.hmm.gz.pfam_sqlite_bulk_load PFAMreference" | sqlite3 Trinotate.sqlite * Running CMD: wget "http://current.geneontology.org/ontology/external2go/pfam2go" --2021-12-21 14:10:59-- http://current.geneontology.org/ontology/external2go/pfam2go Resolving current.geneontology.org (current.geneontology.org)... 143.204.157.188, 143.204.157.220, 143.204.157.96, ... Connecting to current.geneontology.org (current.geneontology.org)|143.204.157.188|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 698981 (683K) [text/plain] Saving to: 'pfam2go' 0K .......... .......... .......... .......... .......... 7% 13.7M 0s 50K .......... .......... .......... .......... .......... 14% 7.21M 0s 100K .......... .......... .......... .......... .......... 21% 13.0M 0s 150K .......... .......... .......... .......... .......... 29% 15.7M 0s 200K .......... .......... .......... .......... .......... 36% 17.7M 0s 250K .......... .......... .......... .......... .......... 43% 27.3M 0s 300K .......... .......... .......... .......... .......... 51% 21.4M 0s 350K .......... .......... .......... .......... .......... 58% 26.2M 0s 400K .......... .......... .......... .......... .......... 65% 50.3M 0s 450K .......... .......... .......... .......... .......... 73% 42.2M 0s 500K .......... .......... .......... .......... .......... 80% 37.7M 0s 550K .......... .......... .......... .......... .......... 87% 42.2M 0s 600K .......... .......... .......... .......... .......... 95% 42.4M 0s 650K .......... .......... .......... .. 100% 140M=0.03s 2021-12-21 14:10:59 (20.9 MB/s) - 'pfam2go' saved [698981/698981] * Running CMD: /usr/local/bin/PFAMtoGoParser.pl pfam2go > pfam2go.tab * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam2go pfam2go.tab CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import pfam2go.tab pfam2go" | sqlite3 Trinotate.sqlite CMD: TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map /corral4/main/objects/b/1/4/dataset_b1441c67-af37-4f06-9a92-e9e489b93fb7.dat --transcript_fasta /corral4/main/objects/7/4/f/dataset_74f49a3b-f8bf-42c0-9072-1e6bdd5ade1f.dat --transdecoder_pep /corral4/main/objects/5/3/c/dataset_53c410f6-44ff-41bd-9a0a-0a7563d1a1e8.dat --bulk_load -parsing gene/trans map file.... done. -loading Transcripts. [100] [200] done. -loading ORFs. done. CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.Transcript.bulk_load Transcript" | sqlite3 Trinotate.sqlite CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.ORF.bulk_load ORF" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/9/9/3/dataset_993670dd-55cc-4ed4-89de-1bb8212b3088.dat --prog blastp --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.2593 BlastDbase" | sqlite3 Trinotate.sqlite BlastDbase loading complete.. CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/1/1/b/dataset_11baa452-88ef-423d-91d7-76469e29485d.dat --prog blastx --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.2775 BlastDbase" | sqlite3 Trinotate.sqlite BlastDbase loading complete.. CMD: Trinotate_PFAM_loader.pl --sqlite Trinotate.sqlite --pfam /corral4/main/objects/4/a/d/dataset_4add977b-1ac7-4f4f-bde8-2365763bdf68.dat CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.pfam_bulk_load.2919 HMMERDbase" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_TMHMM_loader.pl --sqlite Trinotate.sqlite --tmhmm /corral4/main/objects/3/3/6/dataset_3368ab1f-8beb-40cf-9509-ceca6d27d651.dat CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.tmhmm_bulk_load.3108 tmhmm" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_SIGNALP_loader.pl --sqlite Trinotate.sqlite --signalp /corral4/main/objects/b/6/6/dataset_b661a42a-9761-4de8-bf09-7e457f9ca445.dat CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.signalp_bulk_load.3185 signalp" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-05 --pfam_cutoff DNC ``` **Standard Output:** * ```console memory memory memory memory memory memory memory memory memory memory memory memory ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | cond\_download | ` {"__current_case__": 1, "select_download": "yes"} ` | | report\_option | ` {"E": "1e-05", "incl_pep": "false", "incl_trans": "false", "pfam_cutoff": "DNC"} ` | | keep\_sqlite | ` "false" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

• ❌ toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate (Test #2)

  **Problems**: * ``` Output trinotate_out: different than expected Expected file size was 573911, actual file size was 573236 (difference of 100 accepted) ``` **Command Line:** * ```console ``` **Exit Code:** * ```console 0 ``` **Standard Error:** * ```console * Running CMD: wget "http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz" --2021-12-21 13:41:26-- http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74 Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 625798251 (597M) [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' 0K .......... ... 0% 732 =19s 2021-12-21 13:41:46 (732 B/s) - Connection closed at byte 13880. Retrying. --2021-12-21 13:41:47-- (try: 2) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 625784371 (597M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' 0K ,,,,,,,,,, ,,,....... .......... .......... .......... 0% 7.06K 32h59m 50K .......... .......... .......... .......... .......... 0% 409K 14h8m 100K .......... .......... .......... .......... .......... 0% 422K 9h6m 150K .......... .......... .......... .......... .......... 0% 414K 6h46m 200K .......... .......... .......... .......... .......... 0% 407K 5h25m 250K .......... .......... .......... .......... .......... 0% 1.30M 4h30m 300K .......... .......... .......... .......... .......... 0% 421K 3h53m 350K .......... .......... .......... .......... .......... 0% 400K 3h26m 400K .......... .......... .......... .......... .......... 0% 611K 3h4m 450K .......... .......... .......... .......... .......... 0% 353K 2h48m 500K .......... .......... .......... .......... .......... 0% 29.4K 3h5m 550K .......... .......... .......... .......... .......... 0% 417K 2h51m 600K .......... .......... .......... .......... .......... 0% 1.91M 2h38m 650K .......... .......... .......... .......... .......... 0% 390K 2h28m 700K .......... .......... .......... .......... .......... 0% 318K 2h20m 750K .......... .......... .......... .......... .......... 0% 683K 2h12m 800K .......... .......... .......... .......... .......... 0% 519K 2h6m 850K .......... .......... .......... .......... .......... 0% 703K 1h59m 900K .......... .......... .......... .......... .......... 0% 304K 1h55m 950K .......... .......... .......... .......... .......... 0% 546K 1h50m 1000K .......... .......... .......... .......... .......... 0% 34.3K 1h59m 1050K .......... .......... .......... .......... .......... 0% 62.6M 1h53m 1100K .......... .......... .......... .......... .......... 0% 311K 1h50m 1150K .......... .......... .......... .......... .......... 0% 421K 1h46m 1200K .......... .......... .......... .......... .......... 0% 467K 1h43m 1250K .......... .......... .......... .......... .......... 0% 456K 99m59s 1300K .......... .......... .......... .......... .......... 0% 1.18M 96m33s 1350K .......... .......... .......... .......... .......... 0% 253K 94m30s 1400K .......... .......... .......... .......... .......... 0% 1.18M 91m30s 1450K .......... .......... .......... .......... .......... 0% 416K 89m14s 1500K .......... .......... .......... .......... .......... 0% 635K 86m51s 1550K .......... .......... .......... .......... .......... 0% 18.2K 1h41m 1600K .......... .......... .......... .......... .......... 0% 416K 99m18s 1650K .......... .......... .......... .......... .......... 0% 441K 97m2s 1700K .......... .......... .......... .......... .......... 0% 420K 94m56s 1750K .......... .......... .......... .......... .......... 0% 1.36M 92m28s 1800K .......... .......... .......... .......... .......... 0% 416K 90m36s 1850K .......... .......... .......... .......... .......... 0% 417K 88m51s 1900K .......... .......... .......... .......... .......... 0% 586K 86m59s 1950K .......... .......... .......... .......... .......... 0% 419K 85m24s 2000K .......... .......... .......... .......... .......... 0% 1.25M 83m30s 2050K .......... .......... .......... .......... .......... 0% 13.0K 1h40m 2100K .......... .......... .......... .......... .......... 0% 417K 98m21s 2150K .......... .......... .......... .......... .......... 0% 417K 96m39s 2200K .......... .......... .......... .......... .......... 0% 44.6M 94m30s 2250K .......... .......... .......... .......... .......... 0% 399K 92m59s 2300K .......... .......... .......... .......... .......... 0% 367K 91m34s 2350K .......... .......... .......... .......... .......... 0% 481K 90m5s 2400K .......... .......... .......... .......... .......... 0% 438K 88m42s 2450K .......... .......... .......... .......... .......... 0% 1.66M 87m2s 2500K .......... .......... .......... .......... .......... 0% 409K 85m48s 2550K .......... .......... .......... .......... .......... 0% 5.84K 1h57m 2600K .......... .......... .......... .......... .......... 0% 1.21M 1h55m 2650K .......... .......... .......... .......... .......... 0% 1.05M 1h53m 2700K .......... .......... .......... .......... .......... 0% 437K 1h51m 2750K .......... .......... .......... .......... .......... 0% 414K 1h50m 2800K .......... .......... .......... .......... .......... 0% 414K 1h48m 2850K .......... .......... .......... .......... .......... 0% 620K 1h47m 2900K .......... .......... .......... .......... .......... 0% 641K 1h45m 2950K .......... .......... .......... .......... .......... 0% 529K 1h44m 3000K .......... .......... .......... .......... .......... 0% 338K 1h43m 3050K .......... .......... .......... .......... .......... 0% 3.90K 2h23m 3100K .......... .......... .......... .......... .......... 0% 155M 2h21m 3150K .......... .......... .......... .......... .......... 0% 416K 2h19m 3200K ....... 0% 92.9M=44s 2021-12-21 13:42:31 (72.9 KB/s) - Connection closed at byte 3284256. Retrying. --2021-12-21 13:42:33-- (try: 3) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 622513995 (594M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 3200K ] 3200K ,,,,,,,... .......... .......... .......... .......... 0% 5.18K 38h7m 3250K .......... .......... .......... .......... .......... 0% 1.04M 17h39m 3300K .......... .......... .......... .......... .......... 0% 681K 11h33m 3350K .......... .......... .......... .......... .......... 0% 6.26K 15h32m 3400K .......... .......... .......... .......... .......... 0% 417K 12h25m 3450K .......... .......... .......... .......... .......... 0% 416K 10h22m 3500K .......... .......... .......... .......... .......... 0% 154M 8h51m 3550K .......... .......... .......... .......... .......... 0% 416K 7h46m 3600K .......... .......... .......... .......... .......... 0% 416K 6h56m 3650K .......... .......... .......... .......... .......... 0% 401K 6h17m 3700K .......... .......... .......... .......... .......... 0% 6.39K 8h8m 3750K .......... .......... .......... .......... .......... 0% 417K 7h29m 3800K .......... .......... .......... .......... .......... 0% 417K 6h56m 3850K .......... .......... .......... .......... .......... 0% 5.31K 8h43m 3900K .......... .......... .......... .......... .......... 0% 940K 8h8m 3950K .......... .......... .......... .......... .......... 0% 1.74M 7h38m 4000K .......... .......... .......... .......... .......... 0% 417K 7h12m 4050K .......... .......... .......... .......... .......... 0% 411K 6h49m 4100K .......... .......... .......... .......... .......... 0% 549K 6h29m 4150K .......... .......... .......... .......... .......... 0% 417K 6h10m 4200K .......... .......... .......... .......... .......... 0% 4.97K 7h30m 4250K .......... .......... .......... .......... .......... 0% 153K 7h12m 4300K .......... .......... .......... .......... .......... 0% 254M 6h53m 4350K .......... .......... .......... .......... .......... 0% 3.51K 8h37m 4400K .......... .......... .......... .......... .......... 0% 836K 8h16m 4450K .......... .......... ... 0% 8.76M=61s 2021-12-21 13:43:35 (20.7 KB/s) - Connection closed at byte 4580756. Retrying. --2021-12-21 13:43:38-- (try: 4) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 621217495 (592M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 4450K ] 4450K ,,,,,,,,,, ,,,,,,,,,, ,,,....... ...... 0% 1.21K=11s 2021-12-21 13:43:50 (1.21 KB/s) - Connection closed at byte 4594636. Retrying. --2021-12-21 13:43:54-- (try: 5) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 621203615 (592M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 4450K ] 4450K ,,,,,,,,,, ,,,,,,,,,, ,,,,,,,,,, ,,,,,,.... .......... 0% 6.66K 4d0h 4500K .......... .......... .......... .......... .......... 0% 310K 20h29m 4550K .......... .......... .......... .......... .......... 0% 11.6K 17h51m 4600K .......... .......... .......... .......... .......... 0% 416K 12h30m 4650K .......... .......... .......... .......... .......... 0% 416K 9h39m 4700K .......... .......... .......... .......... .......... 0% 118M 7h49m 4750K .......... .......... .......... .......... .......... 0% 414K 6h38m 4800K .......... .......... .......... .......... .......... 0% 417K 5h46m 4850K .......... .......... .......... .......... .......... 0% 418K 5h7m 4900K .......... .......... .......... .......... .......... 0% 398K 4h37m 4950K .......... .......... .......... .......... .......... 0% 95.1M 4h10m 5000K .......... .......... .......... .......... .......... 0% 10.6K 5h12m 5050K .......... .......... .......... .......... .......... 0% 11.8K 5h57m 5100K .......... .......... .......... .......... .......... 0% 423K 5h31m 5150K .......... .......... .......... .......... .......... 0% 1.12M 5h9m 5200K .......... .......... .......... .......... .......... 0% 533K 4h50m 5250K .......... .......... .......... .......... .......... 0% 472K 4h33m 5300K .......... .......... .......... .......... .......... 0% 420K 4h19m 5350K .......... .......... .......... .......... .......... 0% 1.92M 4h5m 5400K .......... .......... .......... .......... .......... 0% 365K 3h53m 5450K .......... .......... .......... .......... .......... 0% 483K 3h43m 5500K .......... .......... .......... .......... .......... 0% 12.3K 4h11m 5550K .......... .......... .......... .......... .......... 0% 10.0K 4h45m 5600K .......... .......... .......... .......... .......... 0% 11.5M 4h33m 5650K .......... .......... .......... .......... .......... 0% 428K 4h22m 5700K .......... .......... .......... .......... .......... 0% 417K 4h13m 5750K .......... .......... .......... .......... .......... 0% 388K 4h4m 5800K .......... .......... .......... .......... .......... 0% 54.9M 3h55m 5850K .......... .......... .......... .......... .......... 0% 411K 3h48m 5900K .......... .......... .......... .......... .......... 0% 423K 3h41m 5950K .......... .......... .......... .......... .......... 0% 417K 3h34m 6000K .......... .......... .......... .......... .......... 0% 9.59K 4h1m 6050K .......... .......... .......... .......... .......... 0% 417K 3h54m 6100K .......... .......... .......... .......... .......... 1% 6.39K 4h35m 6150K .......... .......... .......... .......... .......... 1% 416K 4h27m 6200K .......... .......... .......... .......... .......... 1% 427K 4h20m 6250K .......... .......... .......... .......... .......... 1% 417K 4h14m 6300K .......... .......... .......... .......... .......... 1% 11.8M 4h7m 6350K .......... .......... .......... .......... .......... 1% 400K 4h1m 6400K .......... .......... .......... .......... .......... 1% 397K 3h56m 6450K .......... .......... .......... .......... .......... 1% 475K 3h50m 6500K .......... .......... .......... .......... .......... 1% 8.51K 4h13m 6550K .......... .......... .......... .......... .......... 1% 494K 4h8m 6600K .......... .......... .......... .......... .......... 1% 5.05K 4h48m 6650K .......... .......... .......... .......... .......... 1% 420K 4h42m 6700K .......... .......... .......... .......... .......... 1% 408K 4h36m 6750K .......... .......... .......... .......... .......... 1% 101M 4h30m 6800K .......... .......... .......... .......... .......... 1% 374K 4h25m 6850K .......... .......... .......... .......... .......... 1% 405K 4h20m 6900K .......... .......... .......... .......... .......... 1% 487K 4h15m 6950K .......... .......... .......... .......... .......... 1% 1.01M 4h10m 7000K .......... .......... .......... .......... .......... 1% 6.08K 4h38m 7050K .......... .......... .......... .......... .......... 1% 7.32M 4h32m 7100K .......... .......... .......... .......... .......... 1% 3.35K 5h24m 7150K ....... 1% 640K=86s 2021-12-21 13:45:20 (31.1 KB/s) - Connection closed at byte 7329540. Retrying. --2021-12-21 13:45:25-- (try: 6) http://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 625798251 (597M), 618468711 (590M) remaining [application/octet-stream] Saving to: 'uniprot_sprot.dat.gz' [ skipping 7150K ] 7150K ,,,,,,,... .......... .......... .......... .......... 1% 221K 53m48s 7200K .......... .......... .......... .......... .......... 1% 416K 37m45s 7250K .......... .......... .......... .......... .......... 1% 152M 24m30s 7300K .......... .......... .......... .......... .......... 1% 416K 24m25s 7350K .......... .......... .......... .......... .......... 1% 416K 24m22s 7400K .......... .......... .......... .......... .......... 1% 416K 24m20s 7450K .......... .......... .......... .......... .......... 1% 417K 24m18s 7500K .......... .......... .......... .......... .......... 1% 113M 21m12s 7550K .......... .......... .......... .......... .......... 1% 415K 21m33s 7600K .......... .......... .......... .......... .......... 1% 415K 21m49s 7650K .......... .......... .......... 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.......... .......... 99% 273M 0s 285600K .......... .......... .......... .......... .......... 99% 35.8M 0s 285650K .......... .......... .......... .......... .......... 99% 160M 0s 285700K .......... .......... .......... .......... .......... 99% 247M 0s 285750K .......... .......... .......... .......... .......... 99% 12.0M 0s 285800K .......... .......... .......... .......... .......... 99% 5.88M 0s 285850K .......... .......... .......... .......... .......... 99% 12.4M 0s 285900K .......... .......... .......... .......... .......... 99% 258M 0s 285950K .......... .......... .......... .......... .......... 99% 88.1M 0s 286000K .......... .......... .......... .......... .......... 99% 288M 0s 286050K .......... .......... .......... .......... .......... 99% 245M 0s 286100K .......... .......... .......... ... 100% 234M=13s 2021-12-21 14:11:19 (22.0 MB/s) - 'Pfam-A.hmm.gz' saved [293000230] * Running CMD: /usr/local/bin/PFAM_dat_parser.pl Pfam-A.hmm.gz [100] [200] [300] [400] [500] [600] [700] [800] [900] [1000] [1100] [1200] [1300] [1400] [1500] [1600] [1700] [1800] [1900] [2000] [2100] [2200] [2300] [2400] [2500] [2600] [2700] [2800] [2900] [3000] [3100] [3200] [3300] [3400] [3500] [3600] [3700] [3800] [3900] [4000] [4100] [4200] [4300] [4400] [4500] [4600] [4700] [4800] [4900] [5000] [5100] [5200] [5300] [5400] [5500] [5600] [5700] [5800] [5900] [6000] [6100] [6200] [6300] [6400] [6500] [6600] [6700] [6800] [6900] [7000] [7100] [7200] [7300] [7400] [7500] [7600] [7700] [7800] [7900] [8000] [8100] [8200] [8300] [8400] [8500] [8600] [8700] [8800] [8900] [9000] [9100] [9200] [9300] [9400] [9500] [9600] [9700] [9800] [9900] [10000] [10100] [10200] [10300] [10400] [10500] [10600] [10700] [10800] [10900] [11000] [11100] [11200] [11300] [11400] [11500] [11600] [11700] [11800] [11900] [12000] [12100] [12200] [12300] [12400] [12500] [12600] [12700] [12800] [12900] [13000] [13100] [13200] [13300] [13400] [13500] [13600] [13700] [13800] [13900] [14000] [14100] [14200] [14300] [14400] [14500] [14600] [14700] [14800] [14900] [15000] [15100] [15200] [15300] [15400] [15500] [15600] [15700] [15800] [15900] [16000] [16100] [16200] [16300] [16400] [16500] [16600] [16700] [16800] [16900] [17000] [17100] [17200] [17300] [17400] [17500] [17600] [17700] [17800] [17900] [18000] [18100] [18200] [18300] [18400] [18500] [18600] [18700] [18800] [18900] [19000] [19100] [19200] [19300] [19400] [19500] [19600] * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam Pfam-A.hmm.gz.pfam_sqlite_bulk_load CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import Pfam-A.hmm.gz.pfam_sqlite_bulk_load PFAMreference" | sqlite3 Trinotate.sqlite * Running CMD: wget "http://current.geneontology.org/ontology/external2go/pfam2go" --2021-12-21 14:11:51-- http://current.geneontology.org/ontology/external2go/pfam2go Resolving current.geneontology.org (current.geneontology.org)... 143.204.157.202, 143.204.157.96, 143.204.157.220, ... Connecting to current.geneontology.org (current.geneontology.org)|143.204.157.202|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 698981 (683K) [text/plain] Saving to: 'pfam2go' 0K .......... .......... .......... .......... .......... 7% 13.3M 0s 50K .......... .......... .......... .......... .......... 14% 6.87M 0s 100K .......... .......... .......... .......... .......... 21% 15.3M 0s 150K .......... .......... .......... .......... .......... 29% 14.6M 0s 200K .......... .......... .......... .......... .......... 36% 22.2M 0s 250K .......... .......... .......... .......... .......... 43% 25.6M 0s 300K .......... .......... .......... .......... .......... 51% 18.4M 0s 350K .......... .......... .......... .......... .......... 58% 46.6M 0s 400K .......... .......... .......... .......... .......... 65% 28.3M 0s 450K .......... .......... .......... .......... .......... 73% 43.4M 0s 500K .......... .......... .......... .......... .......... 80% 54.1M 0s 550K .......... .......... .......... .......... .......... 87% 34.8M 0s 600K .......... .......... .......... .......... .......... 95% 56.4M 0s 650K .......... .......... .......... .. 100% 52.2M=0.03s 2021-12-21 14:11:51 (21.0 MB/s) - 'pfam2go' saved [698981/698981] * Running CMD: /usr/local/bin/PFAMtoGoParser.pl pfam2go > pfam2go.tab * Running CMD: /usr/local/bin/EMBL_dat_to_Trinotate_sqlite_resourceDB.pl --sqlite Trinotate.sqlite --pfam2go pfam2go.tab CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import pfam2go.tab pfam2go" | sqlite3 Trinotate.sqlite CMD: TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map /corral4/main/objects/b/1/4/dataset_b1441c67-af37-4f06-9a92-e9e489b93fb7.dat --transcript_fasta /corral4/main/objects/7/4/f/dataset_74f49a3b-f8bf-42c0-9072-1e6bdd5ade1f.dat --transdecoder_pep /corral4/main/objects/5/3/c/dataset_53c410f6-44ff-41bd-9a0a-0a7563d1a1e8.dat --bulk_load -parsing gene/trans map file.... done. -loading Transcripts. [100] [200] done. -loading ORFs. done. CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.Transcript.bulk_load Transcript" | sqlite3 Trinotate.sqlite CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.ORF.bulk_load ORF" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/9/9/3/dataset_993670dd-55cc-4ed4-89de-1bb8212b3088.dat --prog blastp --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.5749 BlastDbase" | sqlite3 Trinotate.sqlite BlastDbase loading complete.. CMD: Trinotate_BLAST_loader.pl --sqlite Trinotate.sqlite --outfmt6 /corral4/main/objects/1/1/b/dataset_11baa452-88ef-423d-91d7-76469e29485d.dat --prog blastx --dbtype Swissprot CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.blast_bulk_load.5972 BlastDbase" | sqlite3 Trinotate.sqlite BlastDbase loading complete.. CMD: Trinotate_PFAM_loader.pl --sqlite Trinotate.sqlite --pfam /corral4/main/objects/4/a/d/dataset_4add977b-1ac7-4f4f-bde8-2365763bdf68.dat CMD: echo "pragma journal_mode=memory; pragma synchronous=0; pragma cache_size=4000000; .mode tabs .import tmp.pfam_bulk_load.6199 HMMERDbase" | sqlite3 Trinotate.sqlite Loading complete.. CMD: Trinotate_report_writer.pl --sqlite Trinotate.sqlite -E 1e-05 --pfam_cutoff DNC --incl_pep --incl_trans ``` **Standard Output:** * ```console memory memory memory memory memory memory memory memory memory memory ``` **Job Parameters:** * | Job parameter | Parameter value | | ------------- | --------------- | | tmhmm | ` None ` | | signalp | ` None ` | | cond\_download | ` {"__current_case__": 1, "select_download": "yes"} ` | | report\_option | ` {"E": "1e-05", "incl_pep": "true", "incl_trans": "true", "pfam_cutoff": "DNC"} ` | | keep\_sqlite | ` "true" ` | | chromInfo | ` "/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len" ` | | dbkey | ` "?" ` | | \_\_input\_ext | ` "input" ` |

[natefoo]

This is a test data diff error, but the tool runs.