~/Desktop/20200427/20200427_sealice_qualimap.sh /Users/strigg/Desktop/20200427/20200427_sealice_qualimap.sh: line 1: fg: no job control ++ FILES='/Users/strigg/Desktop/20200427/*.bam' ++ for f in '$FILES' ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap bamqc --java-mem-size=44G -nt 28 -bam /Users/strigg/Desktop/20200427/Sealice_F1_S20.dedup.sorted.bam Java memory size is set to 44G Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 47244 Mon Apr 27 13:07:55 PDT 2020 WARNING Output folder already exists, the results will be saved there Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 420 Chunk of reads size: 1000 Number of threads: 28 A Processed 50 out of 420 windows... Processed 100 out of 420 windows... Processed 150 out of 420 windows... Processed 200 out of 420 windows... Processed 250 out of 420 windows... Processed 300 out of 420 windows... Processed 350 out of 420 windows... Processed 400 out of 420 windows... Total processed windows:420 Number of reads: 79611238 Number of valid reads: 79611238 Number of correct strand reads:0 Inside of regions... Num mapped reads: 79611238 Num mapped first of pair: 39805619 Num mapped second of pair: 39805619 Num singletons: 0 Time taken to analyze reads: 490 Computing descriptors... numberOfMappedBases: 9519638551 referenceSize: 506970227 numberOfSequencedBases: 9475215166 numberOfAs: 3762018572 Computing per chromosome statistics... Computing histograms... Overall analysis time: 510 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished ++ for f in '$FILES' ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap bamqc --java-mem-size=44G -nt 28 -bam /Users/strigg/Desktop/20200427/Sealice_F2_S22.dedup.sorted.bam Java memory size is set to 44G Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 47244 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 420 Chunk of reads size: 1000 Number of threads: 28 Processed 50 out of 420 windows... Processed 100 out of 420 windows... Processed 150 out of 420 windows... Processed 200 out of 420 windows... Processed 250 out of 420 windows... Processed 300 out of 420 windows... Processed 350 out of 420 windows... Processed 400 out of 420 windows... Total processed windows:420 Number of reads: 53248360 Number of valid reads: 53248360 Number of correct strand reads:0 Inside of regions... Num mapped reads: 53248360 Num mapped first of pair: 26624180 Num mapped second of pair: 26624180 Num singletons: 0 Time taken to analyze reads: 317 Computing descriptors... numberOfMappedBases: 6199394588 referenceSize: 506970227 numberOfSequencedBases: 6173223853 numberOfAs: 2410240743 Computing per chromosome statistics... Computing histograms... Overall analysis time: 330 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap multi-bamqc --java-mem-size=44G -d /Users/strigg/Desktop/20200427/multiBamqc_data_paths.txt -outdir /Users/strigg/Desktop/20200427 Java memory size is set to 44G Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: multi-bamqc Mon Apr 27 13:22:08 PDT 2020 WARNING Output folder already exists, the results will be saved there Running multi-sample BAM QC Checking input paths Failed to run multi-bamqc java.lang.RuntimeException: The raw data doesn't exist for sample: F1 Folder path:/Users/strigg/Desktop/20200427 Please check raw data directory is present. at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.checkInputPaths(MultisampleBamQcAnalysis.java:769) at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run(MultisampleBamQcAnalysis.java:87) at org.bioinfo.ngs.qc.qualimap.main.MultisampleBamQcTool.execute(MultisampleBamQcTool.java:168) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:190) at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111) bash-3.2$ ~/Desktop/20200427/20200427_sealice_qualimap.sh rm screenlog.0  ls~/Desktop/20200427/20200427_sealice_qualimap2.sh.sh /Users/strigg/Desktop/20200427/20200427_sealice_qualimap.sh: line 1: fg: no job control ++ FILES='/Users/strigg/Desktop/20200427/*.bam' ++ for f in '$FILES' ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap bamqc --java-mem-size=44G -nt 28 -bam /Users/strigg/Desktop/20200427/Sealice_F1_S20.dedup.sorted.bam Java memory size is set to 44G Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 47244 Mon Apr 27 13:23:36 PDT 2020 WARNING Output folder already exists, the results will be saved there Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 420 Chunk of reads size: 1000 Number of threads: 28 ^Cbash-3.2$ bash-3.2$ bash-3.2$ bash-3.2$ ~/Desktop/20200427/20200427_sealice_qualimap.sh rm screenlog.0  l~/Desktop/20200427/20200427_sealice_qualimap2.sh chmod +x ~/Desktop/20200427/20200427_sealice_qualimap2.sh ~/Desktop/20200427/20200427_sealice_qualimap2.sh lsscreen -r 37594.SeaLicQualmap lsless 20200427_sealice_qualimap2.sh svimlsvim 20200427_sealice_qualimap.sh rm multiBamqc_data_paths.txt