{"action":"created","issue":{"url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/4","repository_url":"https://api.github.com/repos/Kingsford-Group/ribomap","labels_url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/4/comments","events_url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/4/events","html_url":"https://github.com/Kingsford-Group/ribomap/issues/4","id":149416905,"number":4,"title":"riboprof Segmentation fault (core dumped)","user":{"login":"vitalyg24","id":8531278,"avatar_url":"https://avatars.githubusercontent.com/u/8531278?v=3","gravatar_id":"","url":"https://api.github.com/users/vitalyg24","html_url":"https://github.com/vitalyg24","followers_url":"https://api.github.com/users/vitalyg24/followers","following_url":"https://api.github.com/users/vitalyg24/following{/other_user}","gists_url":"https://api.github.com/users/vitalyg24/gists{/gist_id}","starred_url":"https://api.github.com/users/vitalyg24/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vitalyg24/subscriptions","organizations_url":"https://api.github.com/users/vitalyg24/orgs","repos_url":"https://api.github.com/users/vitalyg24/repos","events_url":"https://api.github.com/users/vitalyg24/events{/privacy}","received_events_url":"https://api.github.com/users/vitalyg24/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-19T10:29:25Z","updated_at":"2016-04-20T06:17:22Z","closed_at":null,"body":"riboprof compiled with boost 1.59 gcc 5.3.0 on CentOS 6.7 \r\n\r\n./riboprof --fasta ./ref/gencode.v18.pc_transcripts_filter.fa --mrnabam alignment/GSM546921_filtered_sequence_transcript_Aligned.out.bam --ribobam alignment/GSM546920_filtered_sequence_transcript_Aligned.out.bam --min_fplen 25 --max_fplen 36 --offset ./offset.txt --sf sm_quant/quant.sf --tabd_cutoff 0 --out ./outputs/GSM546920_filtered_sequence\r\ncds_range file not provided, assume transcript fasta only contains cds sequences.\r\ngetting transcript info...\r\ntotal number of transcripts in transcriptome: 93863\r\nassigning ribo-seq reads...\r\nconstructing profile class...\r\nnumber of transcripts in profile class: 61083\r\nloading reads from bam...\r\ngetting readlen mapping to P site offset...\r\ngetting alignment records...\r\ntotal number of reads: 8087973\r\ngetting read type and p-sites...\r\ntotal output footprint: 8087973\r\ntotal: 8087973  multi_mapped: 0 (0.00 %)\r\nassigning reads to frame 0 loci...\r\nreads used: 0 reads assigned: 0\r\ntotal input count not matching total assigning count!\r\nassigning reads to frame 1 and 2 loci...\r\nreads used: 0 reads assigned: 0\r\ntotal input count not matching total assigning count!\r\nassigning reads to UTR loci...\r\nreads used: 0 reads assigned: 0\r\ntotal input count not matching total assigning count!\r\nassigning RNA-seq reads...\r\nnumber of transcripts in profile class: 61083\r\nloading reads from bam...\r\ngetting alignment records...\r\ntotal number of reads: 5243688\r\ngetting read type and p-sites...\r\ntotal output footprint: 5243688\r\ntotal: 5243688  multi_mapped: 3907204 (74.51 %)\r\nassigning reads...\r\nreads used: 5243688 reads assigned: 5243688\r\nwrite profile results...\r\nrank transcripts...\r\ntranscripts in rank list: 0\r\nSegmentation fault (core dumped)\r\n\r\n\r\nll outputs/\r\ntotal 13M\r\n-rw------- 1 vitalyg training-wx-grp   0 Apr 19 13:24 GSM546920_filtered_sequence_abundant.list\r\n-rw------- 1 vitalyg training-wx-grp   0 Apr 19 13:24 GSM546920_filtered_sequence.base\r\n-rw------- 1 vitalyg training-wx-grp   0 Apr 19 13:24 GSM546920_filtered_sequence.codon\r\n-rw------- 1 vitalyg training-wx-grp   0 Apr 19 13:24 GSM546920_filtered_sequence_scarce.list\r\n-rw------- 1 vitalyg training-wx-grp 11M Apr 19 13:24 GSM546920_filtered_sequence.stats"},"comment":{"url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/comments/212277388","html_url":"https://github.com/Kingsford-Group/ribomap/issues/4#issuecomment-212277388","issue_url":"https://api.github.com/repos/Kingsford-Group/ribomap/issues/4","id":212277388,"user":{"login":"vitalyg24","id":8531278,"avatar_url":"https://avatars.githubusercontent.com/u/8531278?v=3","gravatar_id":"","url":"https://api.github.com/users/vitalyg24","html_url":"https://github.com/vitalyg24","followers_url":"https://api.github.com/users/vitalyg24/followers","following_url":"https://api.github.com/users/vitalyg24/following{/other_user}","gists_url":"https://api.github.com/users/vitalyg24/gists{/gist_id}","starred_url":"https://api.github.com/users/vitalyg24/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vitalyg24/subscriptions","organizations_url":"https://api.github.com/users/vitalyg24/orgs","repos_url":"https://api.github.com/users/vitalyg24/repos","events_url":"https://api.github.com/users/vitalyg24/events{/privacy}","received_events_url":"https://api.github.com/users/vitalyg24/received_events","type":"User","site_admin":false},"created_at":"2016-04-20T06:17:22Z","updated_at":"2016-04-20T06:17:22Z","body":"Including --cds_range resolved the issue.\r\nThanks."}}