search

ebi-pf-team / interproscan

Genome-scale protein function classification
Apache License 2.0
303 stars 67 forks source link

error in using iprscan5.py #367

Closed zhengyanstu closed 3 months ago

zhengyanstu commented 5 months ago

Dear Developers: I encount error when I try to annotate protein sequences using interproscan5 api. Here are my codes: python iprscan5.py --multifasta test.fasta --email xxx@gmail.com --outformat tsv --maxJobs 25 --useSeqId but it shows:"/nfs/public/rw/es/projects/wp-jdispatcher/sources/prod/jobs/iprscan5/rest/20240603/0600/iprscan5-R20240603-060113-0892-16016260-p1m.params (No such file or directory)" Could you help me solving this problem? thank you.

test.fasta:

nad4 MLEHFCECYSDLSGLILCPVLGSITPLFIPNSRIRPIRLIGLCASLITFLYPPVLRIQFDPSTAKSQFVESLRWLPYENINFDLGIDGISLFFVILTTFLIPICISVGWSGMRSYGKEYITASLIREFLMIAVFRILDPLLFYVFPESVPIPMFIIIGVWGSRQRKIKAAYQFFLYTLLGSVFMLLAILLILFQTGTTDLQILLTTEFSERRQIFLWIAFFASFAVKVPMVPVHIWLPEAHVEAPTAGSVILAGILLKLGTYGFLRFSIPMFPEATLCFTPFIYTLSAIAIIYTSLTTLRQIDLKKIIAYSSVAHMNLVTIGMFSLNIQGIGGSILLMLSHGLVSSALFLCVGVLYDRHKTRLVRYYGGLVSTMPNFSTIFLFLTLANMSLPGTSSFIGEFLILVGAFQRNSLVATLAALGMILGAAYSLWLYNRVVSGNLKPSFLHKFSDPNGREVSIFIPFLVGVVRMGVHPKVFPDRMHTSVSNLVQHGKFH atp6-fragment LIHKFICLYAANSKFSHTLLHSY nad2-fragment MFNLFLAVSPEIFIINATFILLIHGVVFSTSKKLDYPPLVSNVGWLGLLSVLITLLLLAAGAPLLTIAHLFWNNLFRGDNFTYFCQILLLLSTAGTISMCFDSSEQERFDASESIVLIPLPTRSMLFMILAHDSIAMYLAIEPQSLCFYVIAASKRKSEFSTEAGSKYLILGAFSSGILLFGFGLWGLLPSLPLSLLHSFHIPLLCSQLL rpl5-fragment NEFEIFEHIRGFNVTIVTSANTQDETLPPWSGF atp8-fragment MPQLDNSHNSSGHAFSSLLSIFP rps1 MMSIYLSRSFPRSNSSFFLCSGNALQSSVLRLREEMFLVDAGPGTPRICMQDEPTGVPINRATRFENKVGSLDLVAGESLIKEQILERFFIDLVAGESLIKERAAARFNDLVGSTDVVAGEPLLLLPRRFRQNRAWMELNKIWRTNTKVKGFIIEKGKGGYSVAIAGFITFLPFRPLISQRISNDRFTIESINPKRTNIVVF nad5-fragment PLSNFWANSPFVLPKNEILAESEFAAPTITKLIPIPFSTSGASVAYNVNPVADQFQRAFQTSTFCNRLYSFFNKRWFFDQVLNDFLVRSFLRFGYEVSFEALDKGAIEILGPYGISYTFRRLVERISQLQSGFVYHYAFAMLLGLTLFVTFSRMWDSLSSWVGNRAYFIWIVITFYNNKSSQE ccmFc MVQLHNFFFFITSMVVPRGTAAPVLLKWFVSRDVPTGAPSSNGTIIPIPIPSFPLLVYLHSRKFIRPTDGAKSGVLVRASRPILLPDIIGRSSSETRERNASFRFVPVLNFLLLQSKGDFSYLESFCGVFRLLLFRTFFFLPRDRSAKRERARRRKGQTLRPNGNEQRRNDKMRCPGHPHLERRIDGFGPVAFPVPPSSGGPCVGGAPPSIGLEALALPTSRQLMAVGHDYYQKAPIKIHISHGGVCICMLGVLLSNTKKIEFTQRLPLGSELYMEKERCSLRGLDHLHGPTFHSICGNFMIYKPSLTNDRLMLKDEHDESLRADLLPINFPASYENGKLEHFLHRWMKNLEHKNFWLTMFLENRNFRETTSTTEVAIHTNPFTDLYASIGTSSSRTCGWYTTIMKLPFIFFIWIGFMLASLGGSRSLLRQLQKDKLRWNRESSVELIIA cox2 MIVLEWLFLTIAPCDAAEPWQLGSQDAATPTMQGIIDLHHDIFFFLILIFVFVSRILVRALWHFHYKRNPIPQRIVHGTTIEILRTIFPSIIPMFIAIPSFALLYSMDEVVVDPAITIKAIGHQWYRTYEYSDYNSSDEQSLTFDSYTIPEDDPELGQSRLLEVDNRVVVPAKIDLRIIVTPADVPHSWAVPSSGVKCDAVPGRLNQTSISVQREGVYYGQCSEICGTNHAFTPIVVEAVPRKDYGSRVSNQLIPQTGEA ccmC MSVSLLQPSFLMSKTRSYAQILIGFRLFLTAMAIHLSLRVAPLDLQQGGNSRIPYVHVPAARMSILVYIATAINTFLFLLTKHPLFLRSSGTGTEMGAFSTLFTLVTGGFRGRPMWGTFRVWDARLTSVFISFLIYLGALRFQKLPVEPAPISIRAGPIDIPIIKSSVNWWNTSHQPGSISRSGTSIHVPMPIPILSNFANSPFSTRIFFVLETRLPIPSFLESPLTNKIEAREGIPKPSSLAESLCIHD atp4 MRLSSTNMQARKMLFAAILSICASSSKKISIYNEEMIVARCFIGFIIFSRKSLGKTFKVTLDGRIQAIQEESQQFPNPNEVVPPESNEQQRLLRISLRICGTVVESLPMARCAPKCEKTVQALLCRNLNVKSATLPNATSSRRICLQDDLVTGFHFSVSERFVPGCTLKASIVELIREGLAVLRMVRVGGFS nad4L MIISISGIRGILLNRRNIPIMSMPIESMLLAVNSNFLVFSVSSDDMMGQSFASLVPTVAAAESAIGSAIFVITFRVRGTIAVESINSIQG cox1-fragment SISLSAVDSAISSLHLSGTFIITSGTGTDCYH

tgrego commented 5 months ago

Hello, your fasta file in invalid, the description lines need to start with a '>' character (for example, >nad4 should be the first line). With an updated fasta file you can run: python iprscan5.py --sequence test.fasta --email xxx@gmail.com --outformat tsv and you should get the expected result.