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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Segmentation fault after samtools or sambamba read the BAM file #149

Open Calhs opened 1 month ago

Calhs commented 1 month ago

Hi, I have encountered an issue when running my BAM file the error mentioned 'Segmentation fault' after reading the BAM files.

This is my config files: config.txt.txt hg38.len file (the extension file is still .len): hg38.len.txt chrFiles directory: chrFiles.txt

This is the error output: error.txt

When I run samtools view independently, it works fine: samtools.txt (sambamba works independently too, but when run with freec I had the same segmentation fault error)

The BAM file only has 1X coverage on average. I also made sure that the annotation for the chromosome name is similar among the len file, bam file, and fasta file (e.g., '1' instead of 'chr1')

Really appreciate it if you have any suggestions to fix this error. Thanks

valeu commented 3 weeks ago

Hi, I don't see what could go wrong from what you shared. It seems that FREEC can read from the bam file (as it can get the number of reads). Did you manage to solve the issue somehow? Did you manage to run FREEC on another example?

Calhs commented 3 weeks ago

Hi thanks for your reply. I did manage to do it but by converting my bam files into pileup first, then using those as the input.