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
2 answers
Summary:
To run multi-bamqc in qualimap, you should have a bed file containg six columns: You can see the comments here
cat bed3.bed | perl -lane 'print "$F[0]\t$F[1]\t$F[2]\t.\t0\t."' > target.bed #this will contain 6 columns
The file containing name of the sample and paths should be as:
sample_1 /media/User/Data//bam/sample_1.bam #file name with extension `.bam`
and run the following command
qualimap multi-bamqc -r -d bam_file.txt -gff target.bed
Not sure if it is related with copy/paste, but the file target.interval_list does not have any file extension.
Is this file a GFF/GTF or BED file?
Regarding the file bam_file.txt, the first column, I think it is the sample name that you want to give, not necessarily the same as the file name. In the second column you need to specify the bam file (this is my understanding from reading the docs - I never run this specific command), something like this:
sample_1 /media/molmed/Data/PJRCT1/bam/001X1.sorted.deduped.bqsr.bam
If you do not have BAM QC result you might need to specify the -r option:
Raw BAM files are provided as input. If this option is activated BAM QC process first will be run for each sample, then multi-sample analysis will be performed.
Source of this information.
I hope this helps,
António
The separator between both columns is a tab?
Did you try with and without the -r option?
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