{"action":"created","issue":{"url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/11","repository_url":"https://api.github.com/repos/BSSeeker/BSseeker2","labels_url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/11/comments","events_url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/11/events","html_url":"https://github.com/BSSeeker/BSseeker2/issues/11","id":188693362,"number":11,"title":"bs_seeker2-call_methylation.py error report","user":{"login":"Shicheng-Guo","id":6641283,"avatar_url":"https://avatars.githubusercontent.com/u/6641283?v=3","gravatar_id":"","url":"https://api.github.com/users/Shicheng-Guo","html_url":"https://github.com/Shicheng-Guo","followers_url":"https://api.github.com/users/Shicheng-Guo/followers","following_url":"https://api.github.com/users/Shicheng-Guo/following{/other_user}","gists_url":"https://api.github.com/users/Shicheng-Guo/gists{/gist_id}","starred_url":"https://api.github.com/users/Shicheng-Guo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Shicheng-Guo/subscriptions","organizations_url":"https://api.github.com/users/Shicheng-Guo/orgs","repos_url":"https://api.github.com/users/Shicheng-Guo/repos","events_url":"https://api.github.com/users/Shicheng-Guo/events{/privacy}","received_events_url":"https://api.github.com/users/Shicheng-Guo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-11T06:23:30Z","updated_at":"2016-11-15T02:56:40Z","closed_at":null,"body":"Hi, \r\n\r\nI met such problems for bs_seeker2-call_methylation.py. I am appreciated to get some help. Thanks.\r\n\r\n\r\n[shg047@tscc-login2 fastq]$ python /home/shg047/software/BSseeker2/bs_seeker2-call_methylation.py -x -r 5 --rm-CCGG -i T19.bam -o T19.mr --txt\r\n\r\n     BS-Seeker2 v2.0.10 - Nov 5, 2015\r\n\r\n[2016-11-10 22:22:03] sorting BS-Seeker alignments\r\nTraceback (most recent call last):\r\n  File \"/home/shg047/software/BSseeker2/bs_seeker2-call_methylation.py\", line 106, in <module>\r\n    pysam.sort(options.infilename, sorted_input_filename)\r\n  File \"/home/shg047/anaconda2/lib/python2.7/site-packages/pysam/utils.py\", line 75, in __call__\r\n    stderr))\r\npysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\\nUsage: samtools sort [options...] [in.bam]\\nOptions:\\n  -l INT     Set compression level, from 0 (uncompressed) to 9 (best)\\n  -m INT     Set maximum memory per thread; suffix K/M/G recognized [768M]\\n  -n         Sort by read name\\n  -o FILE    Write final output to FILE rather than standard output\\n  -T PREFIX  Write temporary files to PREFIX.nnnn.bam\\n  -@, --threads INT\\n             Set number of sorting and compression threads [1]\\n      --input-fmt-option OPT[=VAL]\\n               Specify a single input file format option in the form\\n               of OPTION or OPTION=VALUE\\n  -O, --output-fmt FORMAT[,OPT[=VAL]]...\\n               Specify output format (SAM, BAM, CRAM)\\n      --output-fmt-option OPT[=VAL]\\n               Specify a single output file format option in the form\\n               of OPTION or OPTION=VALUE\\n      --reference FILE\\n               Reference sequence FASTA FILE [null]\\n'\r\n\r\n\r\nRegards, "},"comment":{"url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/comments/260533248","html_url":"https://github.com/BSSeeker/BSseeker2/issues/11#issuecomment-260533248","issue_url":"https://api.github.com/repos/BSSeeker/BSseeker2/issues/11","id":260533248,"user":{"login":"Shicheng-Guo","id":6641283,"avatar_url":"https://avatars.githubusercontent.com/u/6641283?v=3","gravatar_id":"","url":"https://api.github.com/users/Shicheng-Guo","html_url":"https://github.com/Shicheng-Guo","followers_url":"https://api.github.com/users/Shicheng-Guo/followers","following_url":"https://api.github.com/users/Shicheng-Guo/following{/other_user}","gists_url":"https://api.github.com/users/Shicheng-Guo/gists{/gist_id}","starred_url":"https://api.github.com/users/Shicheng-Guo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Shicheng-Guo/subscriptions","organizations_url":"https://api.github.com/users/Shicheng-Guo/orgs","repos_url":"https://api.github.com/users/Shicheng-Guo/repos","events_url":"https://api.github.com/users/Shicheng-Guo/events{/privacy}","received_events_url":"https://api.github.com/users/Shicheng-Guo/received_events","type":"User","site_admin":false},"created_at":"2016-11-15T02:56:40Z","updated_at":"2016-11-15T02:56:40Z","body":"I see. but I am not python user. I like bismark since I know how to change it since it is completed with perl. but there are two many great features of BSSeeker2, that's why I want to make a try, but actually, BSSeeker spend me lots of time to install, for example, python 2 vs python 3 and pysam versions and so on. \r\n\r\nI am lucky. Now I can use it. "}}
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