{"action":"created","issue":{"url":"https://api.github.com/repos/sharpton/shotmap/issues/7","repository_url":"https://api.github.com/repos/sharpton/shotmap","labels_url":"https://api.github.com/repos/sharpton/shotmap/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/sharpton/shotmap/issues/7/comments","events_url":"https://api.github.com/repos/sharpton/shotmap/issues/7/events","html_url":"https://github.com/sharpton/shotmap/issues/7","id":151704670,"number":7,"title":"Error Exit in microbecensus  ","user":{"login":"amorendt","id":7797505,"avatar_url":"https://avatars.githubusercontent.com/u/7797505?v=3","gravatar_id":"","url":"https://api.github.com/users/amorendt","html_url":"https://github.com/amorendt","followers_url":"https://api.github.com/users/amorendt/followers","following_url":"https://api.github.com/users/amorendt/following{/other_user}","gists_url":"https://api.github.com/users/amorendt/gists{/gist_id}","starred_url":"https://api.github.com/users/amorendt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amorendt/subscriptions","organizations_url":"https://api.github.com/users/amorendt/orgs","repos_url":"https://api.github.com/users/amorendt/repos","events_url":"https://api.github.com/users/amorendt/events{/privacy}","received_events_url":"https://api.github.com/users/amorendt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-28T17:55:23Z","updated_at":"2016-04-28T18:08:13Z","closed_at":null,"body":"Hi,  I recently installed shotmap for one of our users, and when working with them to run an analysis we are getting the output below. Not sure of source of problem, and so far looking through the documentation and the scripts is not getting me anywhere in determining reason for the error exit, so I thought I would send this message looking for assistance. Please let me know if there is any additional information that I can provide. Thanks in advance,  Anita Orendt, CHPC, University of Utah\r\n\r\n]$ more slurm-1153141.err-kp163\r\n>> ARGUMENTS TO shotmap.pl: perl shotmap.pl -i /scratch/general/lustre/u0028729/1153141 -d /scratch/general/lustre/u0028729/shotmap_db --nproc=20\r\n####################################################################\r\n# Initializing the shotmap pipeline (Wed Apr 27 22:21:44 MDT 2016) #\r\n####################################################################\r\n[WARNING]: I don't see a previously created ffdb at /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/ so I will try to create\r\n it.\r\n[NOTE]: Starting a classification run using the following settings:\r\n[NOTE]:    * Database name: <>\r\n##################################################\r\n# LOADING PROJECT (Wed Apr 27 22:21:44 MDT 2016) #\r\n##################################################\r\n[NOTE]: Initialized a parameters xml file here: /scratch/general/lustre/u0028729/1153141/shotmap_ffdb//parameters/parameters.xml\r\n[NOTE]: Processing 1 sample associated with project 1153141 \r\n[NOTE]: Successfully loaded 1 sample associated with the project 1153141 \r\n####################################################\r\n# TRANSLATING READS (Wed Apr 27 22:30:17 MDT 2016) #\r\n####################################################\r\n[NOTE]: Translating reads for sample ID n_albigula_foregut_all\r\n\tWaiting for all local jobs to finish...\r\n\t...metatrans (prodigal) has finished. Proceeding\r\n#######################################################\r\n# RUNNING LOCAL SEARCH (Wed Apr 27 22:36:52 MDT 2016) #\r\n#######################################################\r\n[NOTE]: Running search for sample ID n_albigula_foregut_all\r\n\tWaiting for local jobs to finish...\r\n\t...rapsearch finished. Proceeding\r\n#########################################################\r\n# PARSING SEARCH RESULTS (Thu Apr 28 05:35:34 MDT 2016) #\r\n#########################################################\r\n[NOTE]: Parsing results for sample n_albigula_foregut_all\r\n\tWaiting for local jobs to finish...\r\n\t...search results are parsed. Proceeding.\r\n####################################################\r\n# CLASSIFYING READS (Thu Apr 28 05:52:11 MDT 2016) #\r\n####################################################\r\n[NOTE]: Classification_id: 1\r\n[NOTE]: Classifying reads from flatfile for sample ID n_albigula_foregut_all\r\n\t...classification complete. Classification map located here: /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/output/Classifica\r\ntion_Maps/ClassificationMap_Sample_n_albigula_foregut_all.tab\r\n#################################################################\r\n# ESTIMATING AVERAGE GENOME SIZE (Thu Apr 28 05:54:03 MDT 2016) #\r\n#################################################################\r\nWaiting for microbecensus to finish...\r\n\"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albigula_foregut_all/ags/microbecensus/_mc.tmp.gz /scrat\r\nch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albigula_foregut_all/ags/microbecensus/n_albigula_foregut_all_ags.mc > /scratch/general/lu\r\nstre/u0028729/1153141/shotmap_ffdb/logs/microbecensus/microbecensus_n_albigula_foregut_all.log 2>&1\" unexpectedly returned exit value 1 at /\r\nuufs/chpc.utah.edu/sys/installdir/shotmap/1.0/lib/Shotmap/Run.pm line 3993.\r\n at /uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/scripts/shotmap.pl line 24.\r\n\tmain::__ANON__(\"\\\"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/\"...) called at /uufs/chpc.utah.edu/sys/installdir/sho\r\ntmap/1.0/ext/lib/perl5/Carp.pm line 167\r\n\tCarp::croak(\"\\\"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/\"...) called at /uufs/chpc.utah.edu/sys/installdir/shotma\r\np/1.0/ext/lib/perl5/IPC/System/Simple.pm line 566\r\n\tIPC::System::Simple::_check_exit(\"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/1\"..., 1, ARRAY(0x54e74d8)) called at \r\n/uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/ext/lib/perl5/IPC/System/Simple.pm line 538\r\n\tIPC::System::Simple::_process_child_error(256, \"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/1\"..., ARRAY(0x54e74d8))\r\n called at /uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/ext/lib/perl5/IPC/System/Simple.pm line 238\r\n\tIPC::System::Simple::capture(\"run_microbe_census.py -t 8 /scratch/general/lustre/u0028729/1\"...) called at /uufs/chpc.utah.edu/sys/i\r\nnstalldir/shotmap/1.0/lib/Shotmap/Run.pm line 3993\r\n\tShotmap::Run::run_microbecensus(Shotmap=HASH(0x11acf28), \"/scratch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albig\"..., \"/scrat\r\nch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albig\"..., \"/scratch/general/lustre/u0028729/1153141/shotmap_ffdb/logs/mi\"...) called at /\r\nuufs/chpc.utah.edu/sys/installdir/shotmap/1.0/lib/Shotmap/Results.pm line 345\r\n\tShotmap::Results::estimate_ags(Shotmap=HASH(0x11acf28)) called at /uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/scripts/shotmap.pl \r\nline 77"},"comment":{"url":"https://api.github.com/repos/sharpton/shotmap/issues/comments/215513701","html_url":"https://github.com/sharpton/shotmap/issues/7#issuecomment-215513701","issue_url":"https://api.github.com/repos/sharpton/shotmap/issues/7","id":215513701,"user":{"login":"amorendt","id":7797505,"avatar_url":"https://avatars.githubusercontent.com/u/7797505?v=3","gravatar_id":"","url":"https://api.github.com/users/amorendt","html_url":"https://github.com/amorendt","followers_url":"https://api.github.com/users/amorendt/followers","following_url":"https://api.github.com/users/amorendt/following{/other_user}","gists_url":"https://api.github.com/users/amorendt/gists{/gist_id}","starred_url":"https://api.github.com/users/amorendt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amorendt/subscriptions","organizations_url":"https://api.github.com/users/amorendt/orgs","repos_url":"https://api.github.com/users/amorendt/repos","events_url":"https://api.github.com/users/amorendt/events{/privacy}","received_events_url":"https://api.github.com/users/amorendt/received_events","type":"User","site_admin":false},"created_at":"2016-04-28T18:08:13Z","updated_at":"2016-04-28T18:08:13Z","body":"Tom,  Thanks for the quick response.  Here is the log:\r\n\r\n]$ more microbecensus_n_albigula_foregut_all.log\r\n'import site' failed; use -v for traceback\r\nTraceback (most recent call last):\r\n  File \"/uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/bin/run_microbe_census.py\", line 9, in <module>\r\n    import argparse\r\n  File \"/uufs/chpc.utah.edu/sys/installdir/xalt/2015-10-13/libexec/argparse.py\", line 85, in <module>\r\n    import copy as _copy\r\nImportError: No module named copy\r\n\r\nFrom: Thomas Sharpton [mailto:notifications@github.com]\r\nSent: Thursday, April 28, 2016 11:58 AM\r\nTo: sharpton/shotmap <shotmap@noreply.github.com>\r\nCc: Anita Orendt <Anita.Orendt@utah.edu>; Author <author@noreply.github.com>\r\nSubject: Re: [sharpton/shotmap] Error Exit in microbecensus (#7)\r\n\r\nThanks for this message. Can you please provide me with a copy of this file:\r\n\r\n*/scratch/general/lustre/u0028729/1153141/shotmap_ffdb/logs/microbecensus/microbecensus_n_albigula_foregut_all.log\r\n*\r\n\r\nThat will help me determine what went wrong at this step.\r\n\r\nThanks,\r\nTom\r\n\r\nOn Thu, Apr 28, 2016 at 10:55 AM, amorendt <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n> Hi, I recently installed shotmap for one of our users, and when working\r\n> with them to run an analysis we are getting the output below. Not sure of\r\n> source of problem, and so far looking through the documentation and the\r\n> scripts is not getting me anywhere in determining reason for the error\r\n> exit, so I thought I would send this message looking for assistance. Please\r\n> let me know if there is any additional information that I can provide.\r\n> Thanks in advance, Anita Orendt, CHPC, University of Utah\r\n>\r\n> ]$ more slurm-1153141.err-kp163\r\n>\r\n> ARGUMENTS TO shotmap.pl: perl shotmap.pl -i\r\n> /scratch/general/lustre/u0028729/1153141 -d\r\n> /scratch/general/lustre/u0028729/shotmap_db --nproc=20\r\n> ####################################################################\r\n> Initializing the shotmap pipeline (Wed Apr 27 22:21:44 MDT 2016)\r\n>\r\n> ####################################################################\r\n> [WARNING]: I don't see a previously created ffdb at\r\n> /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/ so I will try to\r\n> create\r\n> it.\r\n> [NOTE]: Starting a classification run using the following settings:\r\n> [NOTE]: * Database name: <>\r\n> ##################################################\r\n> LOADING PROJECT (Wed Apr 27 22:21:44 MDT 2016)\r\n>\r\n> ##################################################\r\n> [NOTE]: Initialized a parameters xml file here:\r\n> /scratch/general/lustre/u0028729/1153141/shotmap_ffdb//parameters/parameters.xml\r\n> [NOTE]: Processing 1 sample associated with project 1153141\r\n> [NOTE]: Successfully loaded 1 sample associated with the project 1153141\r\n> ####################################################\r\n> TRANSLATING READS (Wed Apr 27 22:30:17 MDT 2016)\r\n>\r\n> ####################################################\r\n> [NOTE]: Translating reads for sample ID n_albigula_foregut_all\r\n> Waiting for all local jobs to finish...\r\n> ...metatrans (prodigal) has finished. Proceeding\r\n> #######################################################\r\n> RUNNING LOCAL SEARCH (Wed Apr 27 22:36:52 MDT 2016)\r\n>\r\n> #######################################################\r\n> [NOTE]: Running search for sample ID n_albigula_foregut_all\r\n> Waiting for local jobs to finish...\r\n> ...rapsearch finished. Proceeding\r\n> #########################################################\r\n> PARSING SEARCH RESULTS (Thu Apr 28 05:35:34 MDT 2016)\r\n>\r\n> #########################################################\r\n> [NOTE]: Parsing results for sample n_albigula_foregut_all\r\n> Waiting for local jobs to finish...\r\n> ...search results are parsed. Proceeding.\r\n> ####################################################\r\n> CLASSIFYING READS (Thu Apr 28 05:52:11 MDT 2016)\r\n>\r\n> ####################################################\r\n> [NOTE]: Classification_id: 1\r\n> [NOTE]: Classifying reads from flatfile for sample ID\r\n> n_albigula_foregut_all\r\n> ...classification complete. Classification map located here:\r\n> /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/output/Classifica\r\n> tion_Maps/ClassificationMap_Sample_n_albigula_foregut_all.tab\r\n> #################################################################\r\n> ESTIMATING AVERAGE GENOME SIZE (Thu Apr 28 05:54:03 MDT 2016)\r\n>\r\n> #################################################################\r\n> Waiting for microbecensus to finish...\r\n> \"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albigula_foregut_all/ags/microbecensus/\r\n>\r\n>\r\n>\r\n>\r\n> *mc.tmp.gz /scrat\r\n> ch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albigula_foregut_all/ags/microbecensus/n_albigula_foregut_all_ags.mc\r\n> <http://n_albigula_foregut_all_ags.mc> > /scratch/general/lu\r\n> stre/u0028729/1153141/shotmap_ffdb/logs/microbecensus/microbecensus_n_albigula_foregut_all.log\r\n> 2>&1\" unexpectedly returned exit value 1 at /\r\n> uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/lib/Shotmap/Run.pm\r\n> <http://chpc.utah.edu/sys/installdir/shotmap/1.0/lib/Shotmap/Run.pm> line\r\n> 3993. at /uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/scripts/shotmap.pl\r\n> <http://chpc.utah.edu/sys/installdir/shotmap/1.0/scripts/shotmap.pl> line\r\n> 24. main::__ANON_*(\"\\\"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/\"...) called at /uufs/\r\n> chpc.utah.edu/sys/installdir/sho\r\n> tmap/1.0/ext/lib/perl5/Carp.pm line 167\r\n> Carp::croak(\"\\\"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/\"...) called at /uufs/\r\n> chpc.utah.edu/sys/installdir/shotma\r\n> p/1.0/ext/lib/perl5/IPC/System/Simple.pm line 566\r\n> IPC::System::Simple::_check_exit(\"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/1\"..., 1, ARRAY(0x54e74d8)) called at\r\n> /uufs/\r\n> chpc.utah.edu/sys/installdir/shotmap/1.0/ext/lib/perl5/IPC/System/Simple.pm\r\n> line 538\r\n> IPC::System::Simple::_process_child_error(256, \"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/1\"..., ARRAY(0x54e74d8))\r\n> called at /uufs/\r\n> chpc.utah.edu/sys/installdir/shotmap/1.0/ext/lib/perl5/IPC/System/Simple.pm\r\n> line 238\r\n> IPC::System::Simple::capture(\"run_microbe_census.py -t 8\r\n> /scratch/general/lustre/u0028729/1\"...) called at /uufs/\r\n> chpc.utah.edu/sys/i\r\n> nstalldir/shotmap/1.0/lib/Shotmap/Run.pm line 3993\r\n> Shotmap::Run::run_microbecensus(Shotmap=HASH(0x11acf28),\r\n> \"/scratch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albig\"..., \"/scrat\r\n> ch/general/lustre/u0028729/1153141/shotmap_ffdb/n_albig\"...,\r\n> \"/scratch/general/lustre/u0028729/1153141/shotmap_ffdb/logs/mi\"...) called\r\n> at /\r\n> uufs/chpc.utah.edu/sys/installdir/shotmap/1.0/lib/Shotmap/Results.pm line\r\n> 345\r\n> Shotmap::Results::estimate_ags(Shotmap=HASH(0x11acf28)) called at /uufs/\r\n> chpc.utah.edu/sys/installdir/shotmap/1.0/scripts/shotmap.pl\r\n> line 77\r\n>\r\n> —\r\n> You are receiving this because you are subscribed to this thread.\r\n> Reply to this email directly or view it on GitHub\r\n> <https://github.com/sharpton/shotmap/issues/7>\r\n>\r\n\r\n\r\n\r\n--\r\nThomas J. Sharpton\r\n\r\nAssistant Professor\r\nDepartment of Microbiology\r\nDepartment of Statistics\r\nOregon State University\r\n\r\n(541) 737-8623\r\nthomas.sharpton@gmail.com<mailto:thomas.sharpton@gmail.com>\r\n@tjsharpton\r\nlab.sharpton.org\r\n\r\n\r\n—\r\nYou are receiving this because you authored the thread.\r\nReply to this email directly or view it on GitHub<https://github.com/sharpton/shotmap/issues/7#issuecomment-215510788>\r\n"}}