No TAIR, Uniprot and Interproscan .gaf files created during the aggregate step.

[mwslawinska]

Describe the bug
During the aggregate step, only pannzer, argot and fanngo .gaf files are created (no Interpro, uniprot and arabidopsis tair).

Input File
Cre18.g802155_4532.1.p pacid=52508487 transcript=Cre18.g802155_4532.1 locus=Cre18.g802155_4532 ID=Cre18.g802155_4532.1.v6.1 annot-version=v6.1 assoLoc=4532_18_91121_TE org=Chlamydomonas.reinhardtii.CC-4532
MCHLWEWDADIVILTETKLGPRTRWLKDCLRLENLAYRTITSTKPGTEHYKRRSAGVLMAVSARYHAGGHLHIPPTPPNLLGHLAHCTIRTPHSIPLHILGVYCPEDMPTRRRIYTYCTSTLKSAAAAGEHVLIGGDFNAVLTAADRTGPLDDADRHHARFVSSHRLQRITEPNGTTSMTYYQARDGHPKAISRIDDILICQHTSNALVAAATEPGGNTPTLKVQPSGGLFDHSSVHIHLPTFPMRLWTAPTGNRTGSTTQPPTGPWPQVVLPIPTSTLEAVRTKIEHTLASPIARLAAALQPASTAIRDQVDRYTTGATNATELDTQLRRDPTVQAPNLDALAEQLHDILKDGLNILVDMCPKKPPRTGAFAPRRISKKIRRAHEELRQLRAAIADNDTLHT
Cre18.g802156_4532.1.p pacid=52508488 transcript=Cre18.g802156_4532.1 locus=Cre18.g802156_4532 ID=Cre18.g802156_4532.1.v6.1 annot-version=v6.1 assoLoc=4532_18_91136_TE org=Chlamydomonas.reinhardtii.CC-4532
MAIGAILAALCLPALLRQTANITRHVTATAWHRRHLLLWGAALALTLHSLYLNIPDPCSVEKPHMAILGPTVATSLLSANQTKSLLLAHVPHQPHAAHYVKPTLRGALTIGPAAQPAQASMHTRAPTALHWPPNSNNTYREPQRQHFCSVHALNNSLGLAWLDPLDVLSYAKRVHAHLTATQDPNALFWKDCYCPNSGAFSELLLNHYLYHNATISNIFAYPNRKLIMRRTHFPRLNGDISKEKVLENLPVAARTRGFTVHQYTVRHTIAVRYEAGQWRVIDSVNSPIHNTVLHDNTWNTLDGEVWCLDADMQTRKAIYTYCQQVVGRADACGHHLVTAGDFNAVARAHERDSPIDTADRAHQRFLADSGLRPIRGDTTTTAEWSYEQSRPGMAPYHSRIDDILLCPATRAACTEAREYTSTVAGNFDHKPVHAELLAADLQLWPAPQAGARNPAPQQQTQQRWAEVALPVTQKQLAAAAIRLEEALVEATADLHSATRQATQSIEHALTRHSMDPTGYPASVMHRDLAQDTSIQKADINQLAEQLASALDTGLTCLLEECTRKAPFTGKHHTSRSTARALPEVDAANAAAKLRNEIKACQAEHRQLVADRAKAQREAAATALQHTLATRPAQGHKRIFQKEDMERGLPAVRNPETGEVTTDSTSILAILETHFRKLSAPPRGTRTGDFRLPSNATRGYPFEKADATDQFTLDRNRHPDTHSMLPSMADTANFEQCISHLSRNKATGPDGIPNELLRILPSGMKRNLHCILQIMYVKSQIPETWAASETVLLPKPGDALDIKNKRPIALANTCYKLYTSMLTLGIGELAGPLQLFSEAQEGFRAYCNTERQVLNLVHALEDAALFGKDVYAVYVDYSSAFNTIDQDRLLQIMFDLGLPTDLIRAVRNLYAHATTRIRTEHGSTSAIPIERGTVQGDTLSPVLFILFMEPLVRWLHAGGRGYHYGCLTPSENLQYHCSAAAYADDLAALTNSLDDLQVQCDKIASYAEWASLRVNHTKCATTAIWHDKSRSDPNLDGPTGKATLAAMRRNMTNTIKIGTTPVPYFPPTQPSKYLGV

GOMAP step that crashed (if applicable)
aggregate (it finishes successfully, but without the 3 files)

Attach the output files
Output:
INFO [2023-05-02 16:21] Starting to run the pipline for CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly
INFO [2023-05-02 16:21] Obtaining and aggregating Argot2.5 results
INFO [2023-05-02 16:21] The result file already exists.
INFO [2023-05-02 16:21] Delete /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/tmp/mixed-meth/argot2.5/results/GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.tsv if you want to redownload it
INFO [2023-05-02 16:21] Outfile /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/tmp/mixed-meth/argot2.5/results/GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.tsv already exists.
Please deltreeit to regenerate
INFO [2023-05-02 16:21] Filtering mixed-method GAF
INFO [2023-05-02 16:21] test.pod not present so running command
Rscript code/pipeline/mixed2gaf.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:26] Step completed
INFO [2023-05-02 16:26] test.pod not present so running command
Rscript code/pipeline/filter_mixed.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:29] Step completed
INFO [2023-05-02 16:29] Cleaning and aggregating GAF files
INFO [2023-05-02 16:29] test.pod not present so running command
Rscript code/pipeline/clean_duplicate.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:29] Step completed
INFO [2023-05-02 16:29] test.pod not present so running command
Rscript code/pipeline/clean_redundancy.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:31] Step completed
INFO [2023-05-02 16:31] test.pod not present so running command
Rscript code/pipeline/aggregate_datasets.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:32] Step completed

Log
INFO [2023-05-02 16:21] Starting to run the pipline for CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly
INFO [2023-05-02 16:21] Obtaining and aggregating Argot2.5 results
INFO [2023-05-02 16:21] The result file already exists.
INFO [2023-05-02 16:21] Delete /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/tmp/mixed-meth/argot2.5/results/GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.tsv if you want to redownload it
INFO [2023-05-02 16:21] Outfile /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/tmp/mixed-meth/argot2.5/results/GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.1.tsv already exists.
Please deltreeit to regenerate
INFO [2023-05-02 16:21] Filtering mixed-method GAF
INFO [2023-05-02 16:21] test.pod not present so running command
Rscript code/pipeline/mixed2gaf.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:26] Step completed
INFO [2023-05-02 16:26] test.pod not present so running command
Rscript code/pipeline/filter_mixed.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:29] Step completed
INFO [2023-05-02 16:29] Cleaning and aggregating GAF files
INFO [2023-05-02 16:29] test.pod not present so running command
Rscript code/pipeline/clean_duplicate.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:29] Step completed
INFO [2023-05-02 16:29] test.pod not present so running command
Rscript code/pipeline/clean_redundancy.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:31] Step completed
INFO [2023-05-02 16:31] test.pod not present so running command
Rscript code/pipeline/aggregate_datasets.r /workdir/./GOMAP-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly/CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.all.yml
INFO [2023-05-02 16:32] Step completed

Intermediate outpul file (if applicable)
The following files are present (as expected judging by the test):

• tmp/seqsim/tair: At.TAIR10-vs-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.bl.out, CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly-vs-At.TAIR10.bl.out, CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly-vs-At.TAIR10.rbh.out
• • tmp/seqsim/uniprot: CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly-vs-Plant.UniProt.hc.bl.out, CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly-vs-Plant.UniProt.hc.rbh.out, Plant.UniProt.hc-vs-CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.bl.out
• /tmp/domain/iprs/: CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.go.tsv, CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.tsv

System Details
OS: [Ubuntu]
Version: [4.15.0-88-generic #88-Ubuntu x86_64]
Memory Size: [64GB]

Additional context
Add any other context about the problem here.

[wkpalan]

@mwslawinska,

Can you upload your input fasta and you config files?

[mwslawinska]

config.txt
CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.txt

@wkpalan sorry for the late reply, I was out of office. I attached the files as .txt, because GitHub doesn't accept uploading .yml and .fa files, but the contents of the files are the same as in the config.yml and CreinhardtiiCC_4532_707_v6_1_protein_primaryTranscriptOnly_IUPAConly.fa.