/Users/strigg/Desktop/20200429/20200429_sealice_qualimap.sh: line 1: fg: no job control ++ cd /Users/strigg/Desktop/20200429 ++ wget https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20200427/TG_PE_Calig_Aligned/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam --2020-04-29 18:50:29-- https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20200427/TG_PE_Calig_Aligned/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Resolving gannet.fish.washington.edu... 128.95.149.52 Connecting to gannet.fish.washington.edu|128.95.149.52|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 5718377559 (5.3G) [application/octet-stream] Saving to: ‘Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam’ Sealice_F1_S20_R1_001_val_1_bi 100%[==================================================>] 5.33G 71.0MB/s in 78s 2020-04-29 18:51:47 (69.9 MB/s) - ‘Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam’ saved [5718377559/5718377559] ++ wget https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20200427/TG_PE_Calig_Aligned/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam --2020-04-29 18:51:47-- https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20200427/TG_PE_Calig_Aligned/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Resolving gannet.fish.washington.edu... 128.95.149.52 Connecting to gannet.fish.washington.edu|128.95.149.52|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 3761768587 (3.5G) [application/octet-stream] Saving to: ‘Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam’ Sealice_F2_S22_R1_001_val_1_bi 100%[==================================================>] 3.50G 70.8MB/s in 51s 2020-04-29 18:52:38 (70.1 MB/s) - ‘Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam’ saved [3761768587/3761768587] ++ FILES='/Users/strigg/Desktop/20200429/*.bam' ++ for f in '$FILES' ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap bamqc --java-mem-size=44G -nt 28 -bam /Users/strigg/Desktop/20200429/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam Java memory size is set to 44G Launching application... OpenJDK 64-Bit Server VM warning: Ignoring option MaxPermSize; support was removed in 8.0 QualiMap v.2.2.1 Built on 2016-10-03 18:14 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 47244 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 420 Chunk of reads size: 1000 Number of threads: 28 Processed 50 out of 420 windows... Processed 100 out of 420 windows... Processed 150 out of 420 windows... Processed 200 out of 420 windows... Processed 250 out of 420 windows... Processed 300 out of 420 windows... Processed 350 out of 420 windows... Processed 400 out of 420 windows... Total processed windows:420 Number of reads: 78560122 Number of valid reads: 78560122 Number of correct strand reads:0 Inside of regions... Num mapped reads: 78560122 Num mapped first of pair: 39280061 Num mapped second of pair: 39280061 Num singletons: 0 Time taken to analyze reads: 431 Computing descriptors... numberOfMappedBases: 8345705600 referenceSize: 506970227 numberOfSequencedBases: 8308540717 numberOfAs: 3310635970 Computing per chromosome statistics... Computing histograms... Overall analysis time: 450 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished ++ for f in '$FILES' ++ /Users/Shared/bioinformatics/qualimap_v2.2.1/qualimap bamqc --java-mem-size=44G -nt 28 -bam /Users/strigg/Desktop/20200429/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.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: 52851202 Number of valid reads: 52851202 Number of correct strand reads:0 Inside of regions... Num mapped reads: 52851202 Num mapped first of pair: 26425601 Num mapped second of pair: 26425601 Num singletons: 0 Time taken to analyze reads: 278 Computing descriptors... numberOfMappedBases: 5423561703 referenceSize: 506970227 numberOfSequencedBases: 5401721066 numberOfAs: 2115706099 Computing per chromosome statistics... Computing histograms... Overall analysis time: 290 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 Wed Apr 29 19:05:12 PDT 2020 WARNING Output folder already exists, the results will be saved there Running multi-sample BAM QC Checking input paths Loading sample data Failed to run multi-bamqc java.io.FileNotFoundException: /Users/strigg/Desktop/20200427/genome_results.txt (No such file or directory) at java.base/java.io.FileInputStream.open0(Native Method) at java.base/java.io.FileInputStream.open(FileInputStream.java:219) at java.base/java.io.FileInputStream.(FileInputStream.java:157) at java.base/java.io.FileInputStream.(FileInputStream.java:112) at java.base/java.io.FileReader.(FileReader.java:60) at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.loadSummaryStats(MultisampleBamQcAnalysis.java:190) at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.createSummaryTable(MultisampleBamQcAnalysis.java:267) at org.bioinfo.ngs.qc.qualimap.process.MultisampleBamQcAnalysis.run(MultisampleBamQcAnalysis.java:95) 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)