{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/162","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/162/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/162/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/162/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/162","id":99425731,"number":162,"title":"falcon 0.3 stuck at /1-preads fasta2DB, invalid pacbio headers #solved","user":{"login":"HenrivdGeest","id":2330901,"avatar_url":"https://avatars.githubusercontent.com/u/2330901?v=3","gravatar_id":"","url":"https://api.github.com/users/HenrivdGeest","html_url":"https://github.com/HenrivdGeest","followers_url":"https://api.github.com/users/HenrivdGeest/followers","following_url":"https://api.github.com/users/HenrivdGeest/following{/other_user}","gists_url":"https://api.github.com/users/HenrivdGeest/gists{/gist_id}","starred_url":"https://api.github.com/users/HenrivdGeest/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/HenrivdGeest/subscriptions","organizations_url":"https://api.github.com/users/HenrivdGeest/orgs","repos_url":"https://api.github.com/users/HenrivdGeest/repos","events_url":"https://api.github.com/users/HenrivdGeest/events{/privacy}","received_events_url":"https://api.github.com/users/HenrivdGeest/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-08-06T12:39:33Z","updated_at":"2015-08-06T15:49:52Z","closed_at":null,"body":"First of all, credits for using pypeflow,  it does a good job in tracking any failed jobs!\r\n\r\npypeflow log: (removed some long paths)\r\n\r\n2015-08-06 08:23:54,959 - fc_run - INFO - '..../falcon/1-preads_ovl/pdb_build_done.exit' generated. job: 'prepare_pdb.sh-build_pdb-build_pdb' exited.\r\n2015-08-06 08:23:54,960 - fc_run - WARNING - '....../falcon/1-preads_ovl/pdb_build_done' is missing. job: 'prepare_pdb.sh-build_pdb-build_pdb' failed!\r\n2015-08-06 08:23:54,960 - fc_run - WARNING - '..../falcon/1-preads_ovl/pdb_build_done' is missing. job: 'prepare_pdb.sh-build_pdb-build_pdb' failed!\r\n2015-08-06 08:23:55,148 - pypeflow.controller - INFO - message for task://localhost/build_pdb: 'fail'\r\n\r\nI have the fasta files in 0-rawreads/preads/out.****.fasta:\r\n\r\n85M Aug  6 03:34 out.00001.fasta\r\n......\r\n55M Aug  6 03:29 out.00129.fasta\r\n\r\nwhen running the fasta2DB manually:\r\ngeest008@compute-0-2:~...../falcon/1-preads_ovl$ bash prepare_pdb.sh\r\n.....\r\nfasta2DB -v preads -f...../falcon/1-preads_ovl/input_preads.fofn\r\n.........\r\nAdding 'out.00001' ...\r\nFile out.00001.fasta, Line 1: Pacbio header line format error\r\n\r\n\r\n\r\nWhen looking into this fasta file:\r\n head -n 1...../falcon/0-rawreads/preads/out.00001.fasta\r\n>00000000_0\r\n\r\n\r\nfasta2DB works for the /0-rawreads folder, so originally my fasta header is okay, for example:\r\nhead -n 1 m150607_*_s1_p0.1.subreads.fasta:\r\n>m150607_022705_42179_c100789592550000001823170008251570_s1_p0/12/0_24678 RQ=0.848\r\n\r\n\r\nWhen installing FALCON, I ran the make test command, and the synth example ran normally.\r\nI checked the fasta headers for that example and they are fine:\r\nhead -n 1 ...bin/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads/out.00001.fasta\r\n>prolog/000000000/0_1988\r\n\r\n\r\nWhen comparing the /0-rawreads/preads/cp_0001.sh command with the example, I see one difference:\r\n\r\nMy run:\r\nLA4Falcon -H10000 -fo raw_reads las_files/raw_reads.1.las |  fc_consensus.py --output_multi --min_idt 0.70 --min_cov 2 --local_match_count_threshold 2 --max_n_read 40 --n_core 4 > ....\r\n\r\nexample run:\r\n\r\nLA4Falcon -H1 -fo raw_reads las_files/raw_reads.1.las |  fc_consensus.py --output_multi --min_idt 0.70 --min_cov 1 --local_match_count_threshold 100 --max_n_read 20000 --n_core 0 --output_dformat >\r\n\r\n\r\nMy command is missing the \"--output_dformat\" parameter.\r\n\r\n\r\n\r\nOkay, I solved my own problem. I copied an old falcon.cfg file, but apparently some new options are present. Like the last one.\r\nPlease archive this topic, it might be of use for anyone else getting into the same problem :)\r\n\r\nSolution: Use a new provided .cfg file from the example dir (for example: FALCON-integrate/FALCON-examples/run/synth0/fc_run.cfg) to make sure you use all options!\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/128416170","html_url":"https://github.com/PacificBiosciences/FALCON/issues/162#issuecomment-128416170","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/162","id":128416170,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2015-08-06T15:49:52Z","updated_at":"2015-08-06T15:49:52Z","body":"> My command is missing the \"--output_dformat\" parameter.\r\n\r\nJason, this keeps coming up. Maybe we should make that the default? We could provide \"--old-output-format\" if anybody needs it, but probably nobody would."}}