{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/119","labels_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/119/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/119/comments","events_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/119/events","html_url":"https://github.com/PacificBiosciences/SMRT-Analysis/issues/119","id":38105092,"number":119,"title":"Error during de novo assembly of BAC sequence using the SMRTanalysis AMI","user":{"login":"nldowell","id":768550,"avatar_url":"https://avatars.githubusercontent.com/u/768550?v=3","gravatar_id":"","url":"https://api.github.com/users/nldowell","html_url":"https://github.com/nldowell","followers_url":"https://api.github.com/users/nldowell/followers","following_url":"https://api.github.com/users/nldowell/following{/other_user}","gists_url":"https://api.github.com/users/nldowell/gists{/gist_id}","starred_url":"https://api.github.com/users/nldowell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nldowell/subscriptions","organizations_url":"https://api.github.com/users/nldowell/orgs","repos_url":"https://api.github.com/users/nldowell/repos","events_url":"https://api.github.com/users/nldowell/events{/privacy}","received_events_url":"https://api.github.com/users/nldowell/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/labels/unsolved","name":"unsolved","color":"bfd4f2"}],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":17,"created_at":"2014-07-17T17:16:35Z","updated_at":"2015-02-18T15:08:55Z","closed_at":"2014-08-27T18:13:40Z","body":"Hello All,\r\n\r\nI have sequenced a BAC clone (~130 kb) using PacBio. I want to extract the sequences that contain the BAC vector (contaminants) and perform the assembly with only the BAC insert sequence. \r\n\r\nI had this working previously using the following workflow:\r\n1. Connect to the SMRTanalysis AMI and transfer data\r\n2. Run a RS_HGAP_Assembly_3 using the SMRTportal and raw (unfiltered, vector contaminated sequence.\r\n3. Perform the whitelisting tutorial on the raw data to get a text file of 'movie_name/hole_number' which contains the reads that DO NOT map to vector sequence. \r\n4. Copy the output from HGAP3 to local machine. \r\n5. Open the \"settings.xml\" from the HGAP3 output and edit to add the whitelisting module.\r\n6. Copy the new settings.xml file back to the SMRTanalysis AMI \r\n7. Re-run the assembly from the command line using:\r\nsmrtpipe.py --debug --distribute  --params=settings.xml --output=/home/ubuntu/asmb3 xml:inputC3.xml\r\n\r\nWith my current data the re-assembly using the whitelist (step 7, above) is throwing an error which I include below along the master log file. Note that the error is thrown very early and does not appear (to me) to be related to the addition of whitelisting.\r\n\r\nThanks for any help.\r\n\r\nBest,\r\nNoah\r\n\r\nSTDOUT (I can paste the relevant log files too if that is helpful):\r\n\r\n[INFO] 2014-07-17 16:44:30,543 Successfully found 3 files in xml:inputC3.xml\r\n[INFO] 2014-07-17 16:44:31,801 smrtpipe.py running on ip-10-136-59-104\r\n[INFO] 2014-07-17 16:44:31,801 SMRT Analysis v2.2.0 / SMRTpipe 1.85.133289\r\n[INFO] 2014-07-17 16:44:34,176 Process id 24293\r\n[INFO] 2014-07-17 16:44:40,753 Starting task://Anonymous/P_Fetch/toFofn\r\n[INFO] 2014-07-17 16:44:40,753 task P_Fetch.toFofn successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 0 slots.\r\n[INFO] 2014-07-17 16:44:40,754 Workflow Completion Status 1/76 in (            1%) tasks completed.\r\n[INFO] 2014-07-17 16:44:45,777 Starting task://Anonymous/P_Filter/filter.plsFofn.Scatter\r\n[INFO] 2014-07-17 16:44:45,777 Starting task://Anonymous/P_Fetch/adapterRpt\r\n[INFO] 2014-07-17 16:44:45,777 Starting task://Anonymous/P_Fetch/getChemistry\r\n[INFO] 2014-07-17 16:44:45,777 Starting task://Anonymous/P_Fetch/overviewRpt\r\n[INFO] 2014-07-17 16:44:45,779 task P_Filter.filter.plsFofn.Scatter successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 3 slots.\r\n[INFO] 2014-07-17 16:44:45,779 Workflow Completion Status 2/76 in (            2%) tasks completed.\r\n[INFO] 2014-07-17 16:44:48,208 task P_Fetch.getChemistry successfully completed (0.00 sec (0.00 min)). freed 1 slots, using 2 slots.\r\n[INFO] 2014-07-17 16:44:48,208 Workflow Completion Status 3/76 in (            3%) tasks completed.\r\n[INFO] 2014-07-17 16:44:50,651 task P_Fetch.overviewRpt successfully completed (2.00 sec (0.03 min)). freed 1 slots, using 1 slots.\r\n[INFO] 2014-07-17 16:44:50,651 Workflow Completion Status 4/76 in (            5%) tasks completed.\r\n[INFO] 2014-07-17 16:44:55,677 Starting task://Anonymous/P_Filter/filter_003of003\r\n[INFO] 2014-07-17 16:44:55,677 Starting task://Anonymous/P_Filter/filter_001of003\r\n[INFO] 2014-07-17 16:44:55,677 Starting task://Anonymous/P_Filter/filter_002of003\r\n[ERROR] 2014-07-17 16:44:55,677 *** Failed task task://Anonymous/P_Filter/filter_003of003\r\n[ERROR] 2014-07-17 16:44:55,677 *** Failed task task://Anonymous/P_Filter/filter_001of003\r\n[ERROR] 2014-07-17 16:44:55,678 *** Failed task task://Anonymous/P_Filter/filter_002of003\r\n[INFO] 2014-07-17 16:45:03,100 task P_Fetch.adapterRpt successfully completed (18.00 sec (0.30 min)). freed 1 slots, using 6 slots.\r\n[INFO] 2014-07-17 16:45:03,100 Workflow Completion Status 5/76 in (            6%) tasks completed.\r\n[INFO] 2014-07-17 16:45:03,107 Found 3 failed tasks.\r\n[INFO] 2014-07-17 16:45:03,107 task filter_003of003 FAILED \r\n[INFO] 2014-07-17 16:45:03,107 task filter_002of003 FAILED \r\n[INFO] 2014-07-17 16:45:03,108 task filter_001of003 FAILED \r\nTraceback (most recent call last):\r\n  File \"/opt/smrtanalysis/install/smrtanalysis-2.2.0.133377/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py\", line 634, in execute\r\n    raise WorkflowError(_e_msg)\r\nWorkflowError: task://Anonymous/P_Filter/filter_003of003 Failed task://Anonymous/P_Filter/filter_002of003 Failed task://Anonymous/P_Filter/filter_001of003 Failed\r\nFailed smrtpipe version v1.85.133289 with exit code -1 in 34.80 seconds (0.58 minutes)\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/comments/74879188","html_url":"https://github.com/PacificBiosciences/SMRT-Analysis/issues/119#issuecomment-74879188","issue_url":"https://api.github.com/repos/PacificBiosciences/SMRT-Analysis/issues/119","id":74879188,"user":{"login":"madhubioinfo","id":10958956,"avatar_url":"https://avatars.githubusercontent.com/u/10958956?v=3","gravatar_id":"","url":"https://api.github.com/users/madhubioinfo","html_url":"https://github.com/madhubioinfo","followers_url":"https://api.github.com/users/madhubioinfo/followers","following_url":"https://api.github.com/users/madhubioinfo/following{/other_user}","gists_url":"https://api.github.com/users/madhubioinfo/gists{/gist_id}","starred_url":"https://api.github.com/users/madhubioinfo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/madhubioinfo/subscriptions","organizations_url":"https://api.github.com/users/madhubioinfo/orgs","repos_url":"https://api.github.com/users/madhubioinfo/repos","events_url":"https://api.github.com/users/madhubioinfo/events{/privacy}","received_events_url":"https://api.github.com/users/madhubioinfo/received_events","type":"User","site_admin":false},"created_at":"2015-02-18T15:08:55Z","updated_at":"2015-02-18T15:08:55Z","body":"Is this a problem of any memory?\n\n*Mathu Malar C*\n*Research Scholar at computational Biology and Genomics Lab,*\n*CSIR - Indian Institute of Chemical biology,*\n*kolkata-32*\n\n\nOn Tue, Feb 17, 2015 at 1:26 PM, madhu bioinfo <mmadhubioinfo@gmail.com>\nwrote:\n\n> Hello Mengjuei,\n> When i tried to install as a user it could not able to install since it\n> has to write something in the lib area and i have become super user and did\n> it, and later changed the ownership smrt by chown as they mentioned in the\n> installing procedure and the log files have been posted in the above\n> mentioned link\n>\n>\n> *Mathu Malar C*\n> *Research Scholar at computational Biology and Genomics Lab,*\n> *CSIR - Indian Institute of Chemical biology,*\n> *kolkata-32*\n>\n>\n> On Tue, Feb 17, 2015 at 1:06 PM, Mengjuei Hsieh <notifications@github.com>\n> wrote:\n>\n>> Hi Mathu, If you use the smrtpipe under smrtcmds facility, you don't need\n>> to source/dot the setup.sh.\n>>\n>> There are some possible issue judging from the available information,\n>> which is not much. Is this smrtanalysis installed under a preexisting\n>> account, and is this smrtanalysis patched to current patch file?\n>>\n>> By the way, the github doesn't accept email attachment unfortunately. Do\n>> you mind paste it to gist.github.com (and mention the link here)?\n>>\n>> Best,\n>> --mj\n>> via cellular data\n>>\n>> > On Feb 16, 2015, at 23:09, madhubioinfo <notifications@github.com>\n>> wrote:\n>> >\n>> > Hello Mengjuei,\n>> > even i tried in that way also the following error occurs if i run the\n>> > following command in 2 different machines one is centos SGE cluster and\n>> > another one is ubuntu (98Gb) it throws me a following errors\n>> >\n>> > /share/apps/smrtanalysis/current/etc/setup.sh &&\n>> > /share/apps/smrtanalysis/smrtcmds/bin/smrtpipe\n>> > --params=RS_HGAP_Assembly.3.xml xml:input.xml > smrtpipe.log\n>> > --output=test_out\n>> >\n>> > i have attached both the one named as centos and ubuntu one\n>> >\n>> >\n>> >\n>> > *Mathu Malar C*\n>> > *Research Scholar at computational Biology and Genomics Lab,*\n>> > *CSIR - Indian Institute of Chemical biology,*\n>> > *kolkata-32*\n>> >\n>> >\n>> > On Tue, Feb 17, 2015 at 4:43 AM, Mengjuei Hsieh <\n>> notifications@github.com>\n>> > wrote:\n>> >\n>> > > This is not a way to run smrtpipe in command line, please refer our\n>> fine\n>> > > document at:\n>> > >\n>> https://github.com/PacificBiosciences/SMRT-Analysis/wiki/SMRT-Pipe-Reference-Guide-v2.3.0#CommandLine\n>> > > .\n>> > > In short, you can try to use\n>> > > /share/apps/smrtanalysis/smrtcmds/bin/smrtpipe instead, and you can\n>> get it\n>> > > running.\n>> > >\n>> > > --\n>> > > Reply to this email directly or view it on GitHub\n>> > > <\n>> https://github.com/PacificBiosciences/SMRT-Analysis/issues/119#issuecomment-74587278\n>> >\n>>\n>> > > .\n>> > >\n>> > \\\n>> > Reply to this email directly or view it on GitHub.\n>> >\n>>\n>> --\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/PacificBiosciences/SMRT-Analysis/issues/119#issuecomment-74628098>\n>> .\n>>\n>\n>\n"}}