{"action":"created","comment":{"url":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/pulls/comments/320219048","pull_request_review_id":282925079,"id":320219048,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDMyMDIxOTA0OA==","diff_hunk":"@@ -128,34 +128,10 @@ do\n     fi\n done < \"$fastq_list\"\n \n-###Send the jobs out on the cluster with each sample running in parallel###\n-#qsub -sync y -q all.q -t 1-$(cat $out_jobCntrl/job-control.txt | wc -l) -cwd -o \"$out_qsub\" -e \"$out_qsub\" /nfs/users/nfs_b/bm17/bjm_bin/Sanger-JanOw_SPN-Typer.sh $out_jobCntrl\n-#bsub -G team81 -J SPN_Run[1-$(cat $out_jobCntrl/job-control.txt | wc -l)] -cwd -o ${out_qsub}output.%J -e ${out_qsub}errorfile.%J ./Sanger-JanOw_SPN-Typer.sh $out_jobCntrl\n-#bsub -G team81 -R\"select[mem>10000] rusage[mem=10000]\" -M10000 -J SPN_Run[1-2] -o ${out_qsub}output.%J.%I -e ${out_qsub}errorfile.%J.%I \"sh Sanger-JanOw_SPN-Typer.sh $out_jobCntrl\"\n \n-bsub -G team81 -R\"select[mem>10000] rusage[mem=10000]\" -M10000 -J SPN_Run[1-$(cat $out_jobCntrl/job-control.txt | wc -l)] -o ${out_qsub}output.%J.%I -e ${out_qsub}errorfile.%J.%I \"sh Sanger-JanOw_SPN-Typer.sh $out_jobCntrl\"\n-sleep 30\n+uuid=$(cat /proc/sys/kernel/random/uuid)\n+job_prefix=\"SPN_Run-${uuid}\"\n \n-while [[ $(bjobs -noheader | wc -l) -ne 0 ]]\n-do\n-    jobNum=$(bjobs -noheader | wc -l)\n-    echo \"Jobs are still running | $jobNum\"\n-    sleep 120\n-done\n+bsub -R\"select[mem>10000] rusage[mem=10000]\" -M10000 -J \"${job_prefix}[1-$(cat $out_jobCntrl/job-control.txt | wc -l)]\" -o ${out_qsub}output.%J.%I -e ${out_qsub}errorfile.%J.%I \"sh Sanger-JanOw_SPN-Typer.sh $out_jobCntrl\"\n \n-###Output the emm type/MLST/drug resistance data for this sample to it's results output file###\n-batch_name=$(head -n1 $out_jobCntrl/job-control.txt | awk -F\" \" '{print $5}' | awk -F\"/\" '{print $(NF-2)}')\n-#printf \"Sample\\tSerotype\\tST\\taroe\\tgdh_\\tgki_\\trecP\\tspi_\\txpt_\\tddl_\\tPBP_Code(1A:2B:2X)\\tMisc_Resistance\\tGen_Resistance\\tPlasmid_Target\\n\" >> \"$out_analysis\"/TABLE_SPN_\"$batch_name\"_Typing_Results.txt\n-printf 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>> \"$out_analysis\"/TABLE_SPN_\"$batch_name\"_Typing_Results.txt\n-while read -r line\n-do\n-    batch_name=$(echo $line | awk -F\" \" '{print $5}' | awk -F\"/\" '{print $(NF-2)}')\n-    final_outDir=$(echo $line | awk -F\" \" '{print $5}')\n-    final_result_Dir=$(echo $line | awk -F\" \" '{print $4}')\n-    #cat $final_outDir/SAMPLE_Isolate__Typing_Results.txt >> $final_result_Dir/SAMPL_SPN_\"$batch_name\"_Typing_Results.txt\n-    cat $final_outDir/TABLE_Isolate_Typing_results.txt >> $final_result_Dir/TABLE_SPN_\"$batch_name\"_Typing_Results.txt\n-    if [[ -e $final_outDir/TEMP_newPBP_allele_info.txt ]]\n-    then\n-\tcat $final_outDir/TEMP_newPBP_allele_info.txt >> $final_result_Dir/UPDATR_SPN_\"$batch_name\"_Typing_Results.txt\n-    fi\n-done < $out_jobCntrl/job-control.txt\n+bsub -R\"select[mem>1000] rusage[mem=1000]\" -M1000 -w \"ended(${job_prefix}*)\" -J SPN-merge-${uuid} -o ${out_qsub}merge.o -e ${out_qsub}merge.e Sanger-JanOw_SPN-merge.sh \"$out_jobCntrl\" \"$out_analysis\"","path":"Sanger-JanOw_SPN-wrapr.sh","position":38,"original_position":38,"commit_id":"2887ccaf5f8821d5a43e73f6942c4c06f21d6ecb","original_commit_id":"2887ccaf5f8821d5a43e73f6942c4c06f21d6ecb","user":{"login":"seretol","id":46683698,"node_id":"MDQ6VXNlcjQ2NjgzNjk4","avatar_url":"https://avatars3.githubusercontent.com/u/46683698?v=4","gravatar_id":"","url":"https://api.github.com/users/seretol","html_url":"https://github.com/seretol","followers_url":"https://api.github.com/users/seretol/followers","following_url":"https://api.github.com/users/seretol/following{/other_user}","gists_url":"https://api.github.com/users/seretol/gists{/gist_id}","starred_url":"https://api.github.com/users/seretol/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seretol/subscriptions","organizations_url":"https://api.github.com/users/seretol/orgs","repos_url":"https://api.github.com/users/seretol/repos","events_url":"https://api.github.com/users/seretol/events{/privacy}","received_events_url":"https://api.github.com/users/seretol/received_events","type":"User","site_admin":false},"body":"Submit a summarization (merge) job, depending on the first job array (-w \"ended(${job_prefix}*)\")\r\nThis means we don't need to loop for the bjobs output and sleep\r\nIt also allows the pipeline to be run alongside other lsf jobs without interference.  Monitoring the bjobs output could return jobs that have nothing to do with SPN typing...\r\n","created_at":"2019-09-03T11:18:48Z","updated_at":"2019-09-03T11:18:49Z","html_url":"https://github.com/BenJamesMetcalf/SPN-Resistance_Sanger/pull/1#discussion_r320219048","pull_request_url":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/pulls/1","author_association":"NONE","_links":{"self":{"href":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/pulls/comments/320219048"},"html":{"href":"https://github.com/BenJamesMetcalf/SPN-Resistance_Sanger/pull/1#discussion_r320219048"},"pull_request":{"href":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/pulls/1"}}},"pull_request":{"url":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/pulls/1","id":313539371,"node_id":"MDExOlB1bGxSZXF1ZXN0MzEzNTM5Mzcx","html_url":"https://github.com/BenJamesMetcalf/SPN-Resistance_Sanger/pull/1","diff_url":"https://github.com/BenJamesMetcalf/SPN-Resistance_Sanger/pull/1.diff","patch_url":"https://github.com/BenJamesMetcalf/SPN-Resistance_Sanger/pull/1.patch","issue_url":"https://api.github.com/repos/BenJamesMetcalf/SPN-Resistance_Sanger/issues/1","number":1,"state":"open","locked":false,"title":"Sanger 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Removed hardcoded paths in R scripts\r\n- Added install_path parameter to some R function so external scripts can be called without assumption on the installation directories\r\n- SGE_TASK_ID vs LSB_JOBINDEX\r\nPortability changes\r\n- use of #!/usr/bin/env perl instead of #!/usr/bin/perl\r\nWarning removal in perl scripts:\r\n- Assign empty string value to perl strings to avoid warning\r\nExtractions:\r\n- QC step in separate script (fastqc_step.sh)\r\n- Merge/summary step in separate script (Sanger-JanOw_SPN-merge.sh)\r\nbsub changes:\r\nSubmit the job array and submit a merge job depending on the job array (no longer monitoring the output of 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