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3 hours ago by

India

I am trying to run qualimap on multiple bam file via command.

qualimap multi-bamqc -d bam_file.txt -gff target.interval_list

But it gives an error as follows:

qualimap multi-bamqc -d bam_file.txt -gff target.interval_list 
Java memory size is set to 120000M
Launching application...

OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0
QualiMap v.2.2.1
Built on 2016-10-03 18:14

Selected tool: multi-bamqc
Running multi-sample BAM QC

Checking input paths
Failed to run multi-bamqc
java.lang.RuntimeException: The raw data doesn't exist for sample: 001X1.sorted.deduped.bqsr.bam
Folder path:/media/molmed/Data/PJRCT1/bam
Please check raw data directory is present.

bam_file.txt conatins

head bam_file.txt

001X1.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam
001X2.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam
001M1.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam
001M2.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam
003X3.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam
003M1.sorted.deduped.bqsr.bam   /media/molmed/Data/PJRCT1/bam

I also tried by giving the complete path to the file as /media/molmed/Data/PJRCT1/bam/001X1.sorted.deduped.bqsr.bam

and also by adding / to the folder ends as /media/molmed/Data/PJRCT1/bam/. But all gives the same error



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