payload: {"action":"created","issue":{"url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/326","repository_url":"https://api.github.com/repos/nextgenusfs/funannotate","labels_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/326/labels{/name}","comments_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/326/comments","events_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/326/events","html_url":"https://github.com/nextgenusfs/funannotate/issues/326","id":497122298,"node_id":"MDU6SXNzdWU0OTcxMjIyOTg=","number":326,"title":"Funannotate train crash at Pasa step with iso-seq + RNA-seq","user":{"login":"eyalbenda","id":10514913,"node_id":"MDQ6VXNlcjEwNTE0OTEz","avatar_url":"https://avatars0.githubusercontent.com/u/10514913?v=4","gravatar_id":"","url":"https://api.github.com/users/eyalbenda","html_url":"https://github.com/eyalbenda","followers_url":"https://api.github.com/users/eyalbenda/followers","following_url":"https://api.github.com/users/eyalbenda/following{/other_user}","gists_url":"https://api.github.com/users/eyalbenda/gists{/gist_id}","starred_url":"https://api.github.com/users/eyalbenda/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eyalbenda/subscriptions","organizations_url":"https://api.github.com/users/eyalbenda/orgs","repos_url":"https://api.github.com/users/eyalbenda/repos","events_url":"https://api.github.com/users/eyalbenda/events{/privacy}","received_events_url":"https://api.github.com/users/eyalbenda/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":17,"created_at":"2019-09-23T14:10:06Z","updated_at":"2019-12-24T18:15:43Z","closed_at":null,"author_association":"NONE","body":"I've installed the latest funannotate docker image (changed manually the path to 1.6.0 in the installation instructions). \r\nAm running the following command to assemble a genome using pacbio iso-seq and single end RNA seq as evidence:\r\n\r\n`funannotate train -i Dba.dovetail.masked.fasta -s *.fastq.gz --pacbio_isoseq DbaIsoSeq.fasta --species \"Dunaliella\" --cpus 2 --max_intronlen 30000 -o out`\r\n\r\nHowever, I'm getting a crash in Pasa with the following error:\r\n\r\n> Traceback (most recent call last): \r\n  File \"/home/linuxbrew/funannotate/bin/funannotate-train.py\", line 967, in <module>\r\n    runPASAtrain(genome, trinity_transcripts, cleanTranscripts, os.path.abspath(trinityGFF3), stringtieGTF, args.stranded, args.max_intronlen, args.cpus, organism_name, PASA_tmp)\r\n  File \"/home/linuxbrew/funannotate/bin/funannotate-train.py\", line 405, in runPASAtrain\r\n    with open(os.path.join(folder, pasaDBname+'.pasa_assemblies_described.txt'), 'rU') as description:\r\nIOError: [Errno 2] No such file or directory: 'out/training/pasa/Dunaliella_bardawil.pasa_assemblies_described.txt'\r\n"},"comment":{"url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/comments/568787341","html_url":"https://github.com/nextgenusfs/funannotate/issues/326#issuecomment-568787341","issue_url":"https://api.github.com/repos/nextgenusfs/funannotate/issues/326","id":568787341,"node_id":"MDEyOklzc3VlQ29tbWVudDU2ODc4NzM0MQ==","user":{"login":"eyalbenda","id":10514913,"node_id":"MDQ6VXNlcjEwNTE0OTEz","avatar_url":"https://avatars0.githubusercontent.com/u/10514913?v=4","gravatar_id":"","url":"https://api.github.com/users/eyalbenda","html_url":"https://github.com/eyalbenda","followers_url":"https://api.github.com/users/eyalbenda/followers","following_url":"https://api.github.com/users/eyalbenda/following{/other_user}","gists_url":"https://api.github.com/users/eyalbenda/gists{/gist_id}","starred_url":"https://api.github.com/users/eyalbenda/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eyalbenda/subscriptions","organizations_url":"https://api.github.com/users/eyalbenda/orgs","repos_url":"https://api.github.com/users/eyalbenda/repos","events_url":"https://api.github.com/users/eyalbenda/events{/privacy}","received_events_url":"https://api.github.com/users/eyalbenda/received_events","type":"User","site_admin":false},"created_at":"2019-12-24T18:15:43Z","updated_at":"2019-12-24T18:15:43Z","author_association":"NONE","body":"Don't know if this helps, but searching for these chains in the blat gff yields the following lines:\r\n\r\n> chr05   BLAT    cDNA_match      7337275 7337407 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 1 133 +\r\n> chr05   BLAT    cDNA_match      7337081 7337136 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 134 189 +\r\n> chr05   BLAT    cDNA_match      7335182 7335260 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 190 268 +\r\n> chr05   BLAT    cDNA_match      7334693 7334747 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 269 323 +\r\n> chr05   BLAT    cDNA_match      7333975 7334038 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 324 387 +\r\n> chr05   BLAT    cDNA_match      7333740 7333815 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 388 463 +\r\n> chr05   BLAT    cDNA_match      7333239 7333293 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 464 518 +\r\n> chr05   BLAT    cDNA_match      7332749 7332816 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 519 586 +\r\n> chr05   BLAT    cDNA_match      7332460 7332505 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 587 632 +\r\n> chr05   BLAT    cDNA_match      7330984 7331986 100.00  -       .       ID=blat.proc26359.chain_6280;Target=transcript/2537 633 1635 +\r\n> chr05   BLAT    cDNA_match      7337275 7337389 99.13   -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 1 114 +\r\n> chr05   BLAT    cDNA_match      7337081 7337136 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 115 170 +\r\n> chr05   BLAT    cDNA_match      7335182 7335260 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 171 249 +\r\n> chr05   BLAT    cDNA_match      7334693 7334747 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 250 304 +\r\n> chr05   BLAT    cDNA_match      7333975 7334038 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 305 368 +\r\n> chr05   BLAT    cDNA_match      7333740 7333815 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 369 444 +\r\n> chr05   BLAT    cDNA_match      7333239 7333293 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 445 499 +\r\n> chr05   BLAT    cDNA_match      7332749 7332816 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 500 567 +\r\n> chr05   BLAT    cDNA_match      7332460 7332505 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 568 613 +\r\n> chr05   BLAT    cDNA_match      7331145 7331986 100.00  -       .       ID=blat.proc26359.chain_6281;Target=transcript/3505 614 1455 +\r\n\r\ntranscript/3505 (from __all_transcripts fasta):\r\n\r\n> >transcript/3505\r\n> ATTATTTCCTTTTCAATATCTTTTCTGTTAGGTTTACATCCAGAACCACAACACGGCAAG\r\n> ATGACGCAGCAACCAGCAAACGAAATGGCCATGGACCGCAACGCCTACACCAAGGCCATG\r\n> TTTGGAGCTGACAAAGCCTTTGGTACACTTGTGGCTGCGGACAAGAAGCGGGTTGCAGAC\r\n> AAGATGGTGGAGGACGAGATCAAGTCTGCTGGCTCCCTTGTCCCAGGATGTGAAGCTGCA\r\n> CTCGCCAAGGCGGCAGCGGATGCCAGCTTGGAGGCCAAGGAAAGGGACGAAAACTTTGAC\r\n> AGGGATGACTACTCCAAGCGGATTTTTGGACTGCCCTTCAAGCAGCTGTCTGCTGAGCAC\r\n> AAGGAGCGTGTGGTCAATCAGATGATGATGGACGAGATGCATGCTGGTGGCCACGTGATT\r\n> TCAGAGGAGACAGCGCAAGCAAAGGCCATAGCTGATGCCGAATACAAAGCGAGAAACATG\r\n> CACGCGCCGCCTCCTTCAGGTCATTTCATGGTTGGTGGGCATGATCTCCGGAGCCCTGCA\r\n> ACTCCTGGAGGAACAGCTGAAGCCAAGGGGGCTTCTGAGGAGGAGAAGAACAAGCAAAGC\r\n> ACACCGCAAGCAGGGCACATGTTTGTCGCTGGGCACGATCTCAGGACCCCAGGCTCAGGA\r\n> GGCGCAGGTGTCAGACCTGACGAGCTGAACGAAAAAGAGATGAATAAAGCTTTCTAGATC\r\n> TGGCTTGTTGGTAAATTGGTGAAGGGGTGCACCTTTGCCTGCGCTATGTGCTTTGGCTAA\r\n> CATGTGGTGAGGGGTCTGGCGTTTACGAGGAAGGCCAAGAAGGACAGCCTTCAATCTGTG\r\n> CATTCTTGATTCACTTCTTGCATGTTTGCATTCTGAGTGCACAATTTCAGCACTCTTGTA\r\n> CATTCAGTCAATACATGCTTTGGCTAGCAGGTGGAAGTATGCAACCAGTGCACTTGAAGA\r\n> CAAATTCCAGTTAAGCAATTTGACGTACAAGGAAATCCAAAGAGAAGAGCCTTTGAATTT\r\n> TGCACTCTTGATTTACTTCTTGCATGTTTGCATTTCATGCAAATTTGGATCACCCTCTTG\r\n> TATATGACTTTGGTATGTGCTTTGGCTAGCAGGTGGGAGGATGCAAGGAATGAGTGTGTT\r\n> TACGGTCCCACTGCCTTGTTGAGAGGAATAGGCCATCAGCGGCTGCCATTGGTCCCACTG\r\n> CCTTGTTGAGAGGAATAGGCCATCAGCGGCTGCCATTGGGTGTGGAAATCAATAATTTTC\r\n> TGTGGACGCATCAGGGCCATTTTTGTAGAGGTGCAAGGCAACCAGTATACTTGAAGACAT\r\n> GTACCAAATAAGCAAGCATTTGATCCTTTTACAGATCTGAAACAAGTCTAAGGGCTTCTG\r\n> CATTTTTACTTCTTTCATTTTGCATCTCAAACGCAAAATCCCAGCAACCTCTTCAACATT\r\n> AAGTCAATGTTTGGC\r\n\r\ntranscript/2537 is the following:\r\n\r\n> >transcript/2537\r\n> AAAGATAATTGAACAGGTATTATTTCCTTTTCAATATTCTTTTCTGTTAGGTTTACATCC\r\n> AGAACCACAACACGGCAAGATGACGCAGCAACCAGCAAACGAAATGGCCATGGACCGCAA\r\n> CGCCTACACCAAGGCCATGTTTGGAGCTGACAAAGCCTTTGGTACACTTGTGGCTGCGGA\r\n> CAAGAAGCGGGTTGCAGACAAGATGGTGGAGGACGAGATCAAGTCTGCTGGCTCCCTTGT\r\n> CCCAGGATGTGAAGCTGCACTCGCCAAGGCGGCAGCGGATGCCAGCTTGGAGGCCAAGGA\r\n> AAGGGACGAAAACTTTGACAGGGATGACTACTCCAAGCGGATTTTTGGACTGCCCTTCAA\r\n> GCAGCTGTCTGCTGAGCACAAGGAGCGTGTGGTCAATCAGATGATGATGGACGAGATGCA\r\n> TGCTGGTGGCCACGTGATTTCAGAGGAGACAGCGCAAGCAAAGGCCATAGCTGATGCCGA\r\n> ATACAAAGCGAGAAACATGCACGCGCCGCCTCCTTCAGGTCATTTCATGGTTGGTGGGCA\r\n> TGATCTCCGGAGCCCTGCAACTCCTGGAGGAACAGCTGAAGCCAAGGGGGCTTCTGAGGA\r\n> GGAGAAGAACAAGCAAAGCACACCGCAAGCAGGGCACATGTTTGTCGCTGGGCACGATCT\r\n> CAGGACCCCAGGCTCAGGAGGCGCAGGTGTCAGACCTGACGAGCTGAACGAAAAAGAGAT\r\n> GAATAAAGCTTTCTAGATCTGGCTTGTTGGTAAATTGGTGAAGGGGTGCACCTTTGCCTG\r\n> CGCTATGTGCTTTGGCTAACATGTGGTGAGGGGTCTGGCGTTTACGAGGAAGGCCAAGAA\r\n> GGACAGCCTTCAATCTGTGCATTCTTGATTCACTTCTTGCATGTTTGCATTCTGAGTGCA\r\n> CAATTTCAGCACTCTTGTACATTCAGTCAATACATGCTTTGGCTAGCAGGTGGAAGTATG\r\n> CAACCAGTGCACTTGAAGACAAATTCCAGTTAAGCAATTTGACGTACAAGGAAATCCAAA\r\n> GAGAAGAGCCTTTGAATTTTGCACTCTTGATTTACTTCTTGCATGTTTGCATTTCATGCA\r\n> AATTTGGATCACCCTCTTGTATATGACTTTGGTATGTGCTTTGGCTAGCAGGTGGGAGGA\r\n> TGCAAGGAATGAGTGTGTTTACGGTCCCACTGCCTTGTTGAGAGGAATAGGCCATCAGCG\r\n> GCTGCCATTGGTCCCACTGCCTTGTTGAGAGGAATAGGCCATCAGCGGCTGCCATTGGGT\r\n> GTGGAAATCAATAATTTTCTGTGGACGCATCAGGGCCATTTTTGTAGAGGTGCAAGGCAA\r\n> CCAGTATACTTGAAGACATGTACCAAATAAGCAAGCATTTGATCCTTTTACAGATCTGAA\r\n> ACAAGTCTAAGGGCTTCTGCATTTTTACTTCTTTCATTTTGCATCTCAAACGCAAAATCC\r\n> CAGCAACCTCTTCAACATTAAGTCAATGTTTGGCACTTGCGCGATGGATCAAGCTCCCAT\r\n> GACATGAGCGGCGAAGCCAGCATCCAATTACAAGGAAGCAGGATGTGTGGTGTTTCAATT\r\n> CAGATTGGCAATTCAGTTTGAAAGAGCTGAAGCACCTCATGCTCTTTCAAACAACCTGTA\r\n> ACAGTGGAAAATGAG"}}
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