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Dill-PICL / GOMAP-singularity

GOMAP-Singularity is the containerized version of GOMAP
http://gomap.blunderingbioinformatics.org/
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No TAIR, Uniprot and Interproscan .gaf files created during the aggregate step. #35

Open mwslawinska opened 1 year ago

mwslawinska commented 1 year ago

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):

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 commented 1 year ago

@mwslawinska,

Can you upload your input fasta and you config files?

mwslawinska commented 1 year ago

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.