{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/308","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/308/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/308/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/308/events","html_url":"https://github.com/marbl/canu/issues/308","id":193948876,"number":308,"title":"Get polyG/A/T reads after trimming","user":{"login":"WeichenZhou","id":15823356,"avatar_url":"https://avatars.githubusercontent.com/u/15823356?v=3","gravatar_id":"","url":"https://api.github.com/users/WeichenZhou","html_url":"https://github.com/WeichenZhou","followers_url":"https://api.github.com/users/WeichenZhou/followers","following_url":"https://api.github.com/users/WeichenZhou/following{/other_user}","gists_url":"https://api.github.com/users/WeichenZhou/gists{/gist_id}","starred_url":"https://api.github.com/users/WeichenZhou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WeichenZhou/subscriptions","organizations_url":"https://api.github.com/users/WeichenZhou/orgs","repos_url":"https://api.github.com/users/WeichenZhou/repos","events_url":"https://api.github.com/users/WeichenZhou/events{/privacy}","received_events_url":"https://api.github.com/users/WeichenZhou/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2016-12-07T03:27:06Z","updated_at":"2016-12-12T16:02:21Z","closed_at":null,"body":"Dear Sir,\r\nI just started to use CANU and wanted to analyze Human Genome PacBio data.\r\nSo I used the scripts step by step as following:\r\ncorrecting..\r\n`./canu  useGrid=true gridEngine=\"pbs\" gridOptionsJobName=\"canu_test1\" gridEngineThreadsOption=\"-l nodes=3:ppn=4\" gridEngineMemoryOption=\"-l pmem=4gb,qos=flux,wall time=100:00:00\" gridOptions=\"-m abe -V -d . \"  -correct -d 16.12.05.canu_consensus -p wash genomeSize=3g -pacbio-raw SRR1.fastq`\r\nthen trimming..\r\n`./canu  useGrid=true gridEngine=\"pbs\" gridOptionsJobName=\"canu_test_trim1\" gridEngineThreadsOption=\"-l nodes=3:ppn=4\" gridEngineMemoryOption=\"-l pmem=4gb,qos=flux, walltime=100:00:00\" gridOptions=\"-m abe -V -d .\"  -trim -d 16.12.05.canu_consensus -p wash genomeSize=3g -pacbio-corrected wash.correctedReads.fasta.1.gz`\r\nThe corrected fasta.gz looks pretty good, which has 20k number of reads for this SRR1.fastq file. While the trimmed fasta.gz contains reads only having ployT/A/G, and the number decreases to 9k.\r\nBesides, SRR1.fastq is just one of 200 human genome PacBio sequencing files and has 50k raw reads.\r\nHave you ever met that problem before? I would appreciate if you can give some advice to handle this. Thank you so much!\r\n\r\nArthur"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/266469574","html_url":"https://github.com/marbl/canu/issues/308#issuecomment-266469574","issue_url":"https://api.github.com/repos/marbl/canu/issues/308","id":266469574,"user":{"login":"WeichenZhou","id":15823356,"avatar_url":"https://avatars.githubusercontent.com/u/15823356?v=3","gravatar_id":"","url":"https://api.github.com/users/WeichenZhou","html_url":"https://github.com/WeichenZhou","followers_url":"https://api.github.com/users/WeichenZhou/followers","following_url":"https://api.github.com/users/WeichenZhou/following{/other_user}","gists_url":"https://api.github.com/users/WeichenZhou/gists{/gist_id}","starred_url":"https://api.github.com/users/WeichenZhou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/WeichenZhou/subscriptions","organizations_url":"https://api.github.com/users/WeichenZhou/orgs","repos_url":"https://api.github.com/users/WeichenZhou/repos","events_url":"https://api.github.com/users/WeichenZhou/events{/privacy}","received_events_url":"https://api.github.com/users/WeichenZhou/received_events","type":"User","site_admin":false},"created_at":"2016-12-12T16:02:21Z","updated_at":"2016-12-12T16:02:21Z","body":"Thank you so much for your reply.\r\nIn 0-mercounts directory, there are only 3 files: `meryl.1.out-1`  `meryl.jobSubmit.sh`  and `meryl.sh`. \r\nAs in my PBS reports, it looks like CANU run and got output `meryl.$PBS_ARRAYID.out-1`, and then tried to run and failed, error output `canu.01.out`. However, CANU tried another time to submit jobs, failed and have `meryl.$PBS_ARRAYID.out-1` and `canu.01.out` again. It cost a couple of hours to get `meryl.$PBS_ARRAYID.out-1`, but `canu.01.out` only several seconds. I am not sure which stage it failed, but I would like to try a large memory.\r\n-Arthur"}}
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