{"action":"opened","issue":{"url":"https://api.github.com/repos/jdaron/epiTEome/issues/5","repository_url":"https://api.github.com/repos/jdaron/epiTEome","labels_url":"https://api.github.com/repos/jdaron/epiTEome/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/jdaron/epiTEome/issues/5/comments","events_url":"https://api.github.com/repos/jdaron/epiTEome/issues/5/events","html_url":"https://github.com/jdaron/epiTEome/issues/5","id":325692555,"number":5,"title":"Can't locate object method \"qstring\" via package \"Bio::DB::Bam::AlignWrapper\" at epiTEome.pl line 2275.\"","user":{"login":"yq342","id":38974160,"avatar_url":"https://avatars1.githubusercontent.com/u/38974160?v=4","gravatar_id":"","url":"https://api.github.com/users/yq342","html_url":"https://github.com/yq342","followers_url":"https://api.github.com/users/yq342/followers","following_url":"https://api.github.com/users/yq342/following{/other_user}","gists_url":"https://api.github.com/users/yq342/gists{/gist_id}","starred_url":"https://api.github.com/users/yq342/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yq342/subscriptions","organizations_url":"https://api.github.com/users/yq342/orgs","repos_url":"https://api.github.com/users/yq342/repos","events_url":"https://api.github.com/users/yq342/events{/privacy}","received_events_url":"https://api.github.com/users/yq342/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-05-23T12:55:34Z","updated_at":"2018-05-23T12:55:34Z","closed_at":null,"author_association":"NONE","body":"Dear Professor:\r\n       I meet a error when I run the test program in step 2. I hope you can give me some advice and the computer operating system for me is ubuntu 16.04.\r\n        the issue is that:\r\n\"yangqing@yangqing-Lenovo-G480:~/epiTEome-master/test$ perl epiTEome.pl -gff tair10TEs.gff3 -ref Chr2.epiTEome.masked.fasta -un unmapped.fastq -t teid.lst\r\nPossible precedence issue with control flow operator at epiTEome.pl line 482.\r\nINFO epiTEome.pl Sun May 20 09:29:55 2018 Start program!\r\nINFO epiTEome.pl Sun May 20 09:29:55 2018 Run Module: readGffFile!\r\n\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 STEP 1: read ends mapping.\r\nINFO epiTEome.pl: --> Skiping Step 1: unmapped.step1.sort.bam allready exist.\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: splitFastq!\r\n\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 STEP 2: split-reads mapping.\r\n\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 BATCH #1.\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: selectPairedEndReads !\r\nAT2TE41090 284\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: pairedEndGrab !\r\n/home/yangqing/miniconda2/bin/bamutils filter  unmapped.step1.sort.bam unmapped.matePairedEnd.bam -whitelist  unmapped.fishReads.list\r\nDone! (0:00)                                                                                 \r\n208 kept\r\n775 failed\r\n/home/yangqing/miniconda2/bin/samtools index unmapped.matePairedEnd.bam\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: checkPairedEndPosition !\r\n/home/yangqing/miniconda2/bin/fastqutils filter -whitelist unmapped.step1.list unmapped.fastq  >  unmapped.step1.fastq\r\n112 reads in whitelist\r\nDone! (0:00)                                                             \r\nCriteria Kept Altered Removed\r\nFASTQReader 121 0 0\r\nWhitelistFilter 112 0 9\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: splitFastq!\r\nINFO epiTEome.pl Sun May 20 09:29:58 2018 Run Module: Segemehl mapping !\r\n/usr/bin/segemehl.x --silent -t  1 -D 1 -E  5  -i  Chr2.epiTEome.masked.fasta.ctidx -j Chr2.epiTEome.masked.fasta.gaidx -d Chr2.epiTEome.masked.fasta -q unmapped.step1.sr.fastq -o unmapped.step2.sam  -F 1 2>log\r\n/home/yangqing/miniconda2/bin/samtools view -b unmapped.step2.sam | /home/yangqing/miniconda2/bin/samtools sort - -o unmapped.step2.sort.bam\r\n/home/yangqing/miniconda2/bin/samtools index  unmapped.step2.sort.bam\r\nINFO epiTEome.pl Sun May 20 09:30:02 2018 Run Module: selectSplitReads !\r\nINFO epiTEome.pl Sun May 20 09:30:02 2018 Run Module: splitReadsGrab !\r\n/home/yangqing/miniconda2/bin/bamutils filter  unmapped.step2.sort.bam unmapped.mateSplitReads.bam -whitelist unmapped.fishReads.list\r\nDone! (0:00)                                                                                     \r\n759 kept\r\n3411 failed\r\n/home/yangqing/miniconda2/bin/samtools index unmapped.mateSplitReads.bam\r\nINFO epiTEome.pl Sun May 20 09:30:03 2018 Run Module: groupOverlapingmNeoReads, 103 to process.\r\nINFO epiTEome.pl Sun May 20 09:30:03 2018 Run Module: neoInsertionFinder !\r\nINFO epiTEome.pl: Cleaning file: /bin/rm unmapped.fishReads.list unmapped.matePairedEnd.bam unmapped.matePairedEnd.bam.bai unmapped.mateSplitReads.bam unmapped.mateSplitReads.bam.bai unmapped.pe.fastq unmapped.step1.fastq unmapped.step1.list unmapped.step1.sr.fastq unmapped.step2.sort.bam unmapped.step2.sort.bam.bai\r\nCan't locate object method \"qstring\" via package \"Bio::DB::Bam::AlignWrapper\" at epiTEome.pl line 2275.\"\r\nthank you very much!"}}
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