{"action":"created","issue":{"url":"https://api.github.com/repos/brentp/bwa-meth/issues/27","repository_url":"https://api.github.com/repos/brentp/bwa-meth","labels_url":"https://api.github.com/repos/brentp/bwa-meth/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/brentp/bwa-meth/issues/27/comments","events_url":"https://api.github.com/repos/brentp/bwa-meth/issues/27/events","html_url":"https://github.com/brentp/bwa-meth/issues/27","id":165675367,"number":27,"title":"paired reads not recoqnized as such","user":{"login":"cb4github","id":19474439,"avatar_url":"https://avatars.githubusercontent.com/u/19474439?v=3","gravatar_id":"","url":"https://api.github.com/users/cb4github","html_url":"https://github.com/cb4github","followers_url":"https://api.github.com/users/cb4github/followers","following_url":"https://api.github.com/users/cb4github/following{/other_user}","gists_url":"https://api.github.com/users/cb4github/gists{/gist_id}","starred_url":"https://api.github.com/users/cb4github/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cb4github/subscriptions","organizations_url":"https://api.github.com/users/cb4github/orgs","repos_url":"https://api.github.com/users/cb4github/repos","events_url":"https://api.github.com/users/cb4github/events{/privacy}","received_events_url":"https://api.github.com/users/cb4github/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-07-14T22:44:17Z","updated_at":"2016-07-18T20:51:08Z","closed_at":null,"body":"Dear brentp,\r\n\r\nHere's my SLURM script:\r\n#!/bin/bash\r\n#SBATCH --job-name=bwa-meth   ### Job Name\r\n#SBATCH --output=bwa-meth24hr.out    ### File in which to store job output\r\n#SBATCH --error=bwa-meth24hr.err     ### File in which to store job error messages\r\n#SBATCH --qos=normal            ### Quality of Service (like a queue in PBS)\r\n#SBATCH --time=0-24:00:00       ### Wall clock time limit in Days-HH:MM:SS\r\n#SBATCH --nodes=1               ### Node count required for the job\r\n#SBATCH --ntasks-per-node=20        ### Nuber of tasks to be launched per Node\r\n\r\necho pwd=`pwd`\r\nmodule load python/2.7.11\r\nmodule load samtools\r\nREFERENCE=/lustre/project/hpcstaff/user/OryziasLatipes/GCF_000313675.1_ASM31367v1_genomic.fna.bgz\r\necho Generating index for $REFERENCE\r\ntime bwameth.py index $REFERENCE\r\necho Analyzing methylation..\r\ntime bwameth.py --reference $REFERENCE ../sra-toolkit/SRR2050320_1.fastq.gz ../sra-toolkit/SRR2050320_2.fastq.gz -t 20 --read-group $'@RG\\tID:SRR2050320\\tSM:SRR2050320'\r\necho Analysis succeeded.\r\n\r\n...and here's the result of my alignment check...\r\n37067603 + 3256037 in total (QC-passed reads + QC-failed reads)\r\n63598 + 967992 secondary\r\n0 + 0 supplimentary\r\n0 + 0 duplicates\r\n35373511 + 3256037 mapped (95.43%:100.00%)\r\n0 + 0 paired in sequencing\r\n0 + 0 read1\r\n0 + 0 read2\r\n0 + 0 properly paired (-nan%:-nan%)\r\n0 + 0 with itself and mate mapped\r\n0 + 0 singletons (-nan%:-nan%)\r\n0 + 0 with mate mapped to a different chr\r\n0 + 0 with mate mapped to a different chr (mapQ>=5)\r\n\r\nQ: This says zero reads paired, true? Is this correct?\r\n\r\nPlease let me know if you need more info, thanks.\r\n\r\nBest,\r\nCB"},"comment":{"url":"https://api.github.com/repos/brentp/bwa-meth/issues/comments/233454690","html_url":"https://github.com/brentp/bwa-meth/issues/27#issuecomment-233454690","issue_url":"https://api.github.com/repos/brentp/bwa-meth/issues/27","id":233454690,"user":{"login":"brentp","id":1739,"avatar_url":"https://avatars.githubusercontent.com/u/1739?v=3","gravatar_id":"","url":"https://api.github.com/users/brentp","html_url":"https://github.com/brentp","followers_url":"https://api.github.com/users/brentp/followers","following_url":"https://api.github.com/users/brentp/following{/other_user}","gists_url":"https://api.github.com/users/brentp/gists{/gist_id}","starred_url":"https://api.github.com/users/brentp/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brentp/subscriptions","organizations_url":"https://api.github.com/users/brentp/orgs","repos_url":"https://api.github.com/users/brentp/repos","events_url":"https://api.github.com/users/brentp/events{/privacy}","received_events_url":"https://api.github.com/users/brentp/received_events","type":"User","site_admin":false},"created_at":"2016-07-18T20:51:08Z","updated_at":"2016-07-18T20:51:08Z","body":"So you have no paired reads. I would guess that something is wrong with your 2nd fastq file. You can try just aligning that with bwa-meth and see what happens.\r\n\r\nIt could also be that your reads are not from the directional (stranded) protocol and so you might have to use an aligner that supports that. It's most common that they would be directional, but if these are from an old SRA archive, then they might not be."}}
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