{"action":"created","issue":{"url":"https://api.github.com/repos/joshuagryphon/plastid/issues/27","repository_url":"https://api.github.com/repos/joshuagryphon/plastid","labels_url":"https://api.github.com/repos/joshuagryphon/plastid/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/joshuagryphon/plastid/issues/27/comments","events_url":"https://api.github.com/repos/joshuagryphon/plastid/issues/27/events","html_url":"https://github.com/joshuagryphon/plastid/issues/27","id":377207021,"node_id":"MDU6SXNzdWUzNzcyMDcwMjE=","number":27,"title":"could not open alignment file - psite offset","user":{"login":"AnaHowellsFerreira","id":19144074,"node_id":"MDQ6VXNlcjE5MTQ0MDc0","avatar_url":"https://avatars2.githubusercontent.com/u/19144074?v=4","gravatar_id":"","url":"https://api.github.com/users/AnaHowellsFerreira","html_url":"https://github.com/AnaHowellsFerreira","followers_url":"https://api.github.com/users/AnaHowellsFerreira/followers","following_url":"https://api.github.com/users/AnaHowellsFerreira/following{/other_user}","gists_url":"https://api.github.com/users/AnaHowellsFerreira/gists{/gist_id}","starred_url":"https://api.github.com/users/AnaHowellsFerreira/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AnaHowellsFerreira/subscriptions","organizations_url":"https://api.github.com/users/AnaHowellsFerreira/orgs","repos_url":"https://api.github.com/users/AnaHowellsFerreira/repos","events_url":"https://api.github.com/users/AnaHowellsFerreira/events{/privacy}","received_events_url":"https://api.github.com/users/AnaHowellsFerreira/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-04T23:21:49Z","updated_at":"2018-11-09T03:49:53Z","closed_at":"2018-11-07T02:58:08Z","author_association":"NONE","body":"Hi Joshua! \r\n\r\nWe've been working on the psite (subprogram) but have encountered an issue and would appreciate\r\nsome feedback on how to handle this, since it is not very intuitive:\r\n\r\nHere's were we started...\r\n(https://plastid.readthedocs.io/en/latest/examples/p_site.html)\r\n\r\nThe gtf file was obtained from gramene. We did some filtering by removing cp (chloroplast), \r\nmithocondria (mt), tRNA and rRNA reads. \r\n\r\nOur bam file was obtained from STAR after multiple sequential alignments to isolate nuclear genomic reads, and they were sorted in indexed with Samtools: \r\n\r\nsamtools sort --threads 27 ${in_file} -o sorted_${out_filename}\r\nsamtools index ${in_file} -b indexed_${out_filename}\r\n\r\nAfter running the metagene generate on our maize reference and obtaining the *_rois.txt \r\nfile required for the next step (psite), we tested on our indexed bam file but encountered \r\nthe following warning messages:\r\n\r\n\"[E::hts_hopen] Failed to open file indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam\r\n[E::hts_open_format] Failed to open file indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam\r\npsite [2018-11-02 09:59:03]: Opening ROI file Zea_mays_orfs_rois.txt ...\r\npsite [2018-11-02 09:59:04]: Opening count files indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam ...\r\nTraceback (most recent call last):\r\n  File \"/packages/anaconda3/5.1.0/envs/plastid/bin/psite\", line 11, in <module>\r\n    load_entry_point('plastid==0.4.8', 'console_scripts', 'psite')()\r\n  File \"/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/bin/psite.py\", line 326, in main\r\n    ga = ap.get_genome_array_from_args(args,printer=printer)\r\n  File \"/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/util/scriptlib/argparsers.py\", line 572, in get_genome_array_from_args\r\n    count_files = [pysam.Samfile(X,\"rb\") for X in args.count_files]\r\n  File \"/packages/anaconda3/5.1.0/envs/plastid/lib/python3.5/site-packages/plastid/util/scriptlib/argparsers.py\", line 572, in <listcomp>\r\n    count_files = [pysam.Samfile(X,\"rb\") for X in args.count_files]\r\n  File \"pysam/libcalignmentfile.pyx\", line 734, in pysam.libcalignmentfile.AlignmentFile.__cinit__\r\n  File \"pysam/libcalignmentfile.pyx\", line 933, in pysam.libcalignmentfile.AlignmentFile._open\r\nOSError: [Errno 8] could not open alignment file `indexed_cp_genome_102617_RF-15Dark_Rep1_mergedAligned.out.bam`: Exec format error\"\r\n\r\nThe indexed bam files seem to be ok since we ran Subreads (featureCounts) on them, but for some reason, we cannot run plastid on them (counts_file argument, failed to open)\r\n\r\nWe appreciate your feedback and look forward to hearing back from you.\r\n\r\nAna and Mandie"},"comment":{"url":"https://api.github.com/repos/joshuagryphon/plastid/issues/comments/437241153","html_url":"https://github.com/joshuagryphon/plastid/issues/27#issuecomment-437241153","issue_url":"https://api.github.com/repos/joshuagryphon/plastid/issues/27","id":437241153,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNzI0MTE1Mw==","user":{"login":"AnaHowellsFerreira","id":19144074,"node_id":"MDQ6VXNlcjE5MTQ0MDc0","avatar_url":"https://avatars2.githubusercontent.com/u/19144074?v=4","gravatar_id":"","url":"https://api.github.com/users/AnaHowellsFerreira","html_url":"https://github.com/AnaHowellsFerreira","followers_url":"https://api.github.com/users/AnaHowellsFerreira/followers","following_url":"https://api.github.com/users/AnaHowellsFerreira/following{/other_user}","gists_url":"https://api.github.com/users/AnaHowellsFerreira/gists{/gist_id}","starred_url":"https://api.github.com/users/AnaHowellsFerreira/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AnaHowellsFerreira/subscriptions","organizations_url":"https://api.github.com/users/AnaHowellsFerreira/orgs","repos_url":"https://api.github.com/users/AnaHowellsFerreira/repos","events_url":"https://api.github.com/users/AnaHowellsFerreira/events{/privacy}","received_events_url":"https://api.github.com/users/AnaHowellsFerreira/received_events","type":"User","site_admin":false},"created_at":"2018-11-09T03:49:53Z","updated_at":"2018-11-09T03:49:53Z","author_association":"NONE","body":"Oh, no worries! We are enjoying learning about Plastid and quite amused by the program (only a few weeks into Ribo-seq, hehe!). \r\nThank you for the reply and we'll keep you posted on any potential new issues. \r\nHave a good weekend and hopefully some rest from your hectic week  🙃 😊 \r\nAna"}}
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