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aradenbaugh / radia

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
GNU Affero General Public License v3.0
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CRITICAL The index file for the BAM file doesn't exist #8

Closed itamuria closed 5 years ago

itamuria commented 5 years ago

Dear Developer,

I am trying to use RADIA with 2 DNAs and 1 RNA in bam format but I get an error.

The used command line is:

python $radia \ patientId \ chrom \ -n $dnanormal \ -t $dnatumor \ -r $rnatumor \ -f $fastafile \ -o patientId_chr1.vcf.gz \ -i hg38

and the error is the next one:

05/18/2019 12:14:06 AM CRITICAL The index file for the BAM file /home/627_tumor.printed.bam doesn't exist. Please use the 'samtools index' command to create one.

The problem is that I have the index file in .bai format.

Why could be the error? Thanks, All the best, Ibon

aradenbaugh commented 5 years ago

Hi Ibon,

It seems like something is wrong with the bam index file. RADIA expects it to be in the same directory as the .bam file itself. Is your .bai file in the same directory, and is it named /home/627_tumor.printed.bam.bai? If it is, then maybe try recreating the index file.

You can also try running a samtools mpileup command on the bam file directly to test it. If there is a problem with the .bai file, it may give you a more detailed message.

Let me know if you're still having a problem.

Thanks, Amie

itamuria commented 5 years ago

Hi Amie,

Thanks for your reply. I created again the index files and now it works. Thanks, All the best, Ibon