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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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ERROR: Invalid parameters passed to getCandidateBreakPointsDir #24

Open arumds opened 2 years ago

arumds commented 2 years ago

Hi,

I am getting the below error during Calling step:

Command: ./bin/retroseq.pl -call -bam /scratch/G300B1.bam -input /scratch/retroseq/sinec -ref /scratch/l1.0_ROSY.fa -output /scratch/retroseq/sinec.vcf -filter SINEC.refTEs.txt -reads 3 -depth 400

Tail of the error message:

<mpileup> Set max per-file depth to 8000
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
ERROR: Invalid parameters passed to getCandidateBreakPointsDir: chrUn_JAAHUQ010000692v1 -471 282

It progressed to some unplaced chromosomes in non-human genomes and getting the above error. It produced het.bed and hom.bed files before terminating as above. Could you help.

xuxif commented 2 years ago

Author may not still be working on this software. Go to line 921 of retroseq.pl and add ' if($start> $end or $start <0 or $end <0){ next;}' after line 921. The program will skip a few wrong record.

tk2 commented 2 years ago

Hi All - it has been quite a few years since I looked at the code. As a workaround, can you use the -chr parameter to call on the autosomes specifically. I haven't tested what happens with the unplaced chrs, some of them might be very small so cause boundary issues like what you got.