[bed_read] Parse error reading "...slice.bam.gridss.target.bed" at line 1498 : end (5095) must not be less than start (18446744073709546616) #449
Description
After using my workaround in #448, I then came across this issue whilst trying to slice a bam file aligned with hg38 and alt contig. The bam was (sv called by dragen)
I then got this error:
Sat Feb 6 02:46:27 UTC 2021: Using input file "/var/lib/cwl/stg13fa2124-c9c6-42c6-8015-f354f3fbc624/SBJ_seqcii_020.bam"
Sat Feb 6 02:46:27 UTC 2021: Using SVs in /var/lib/cwl/stgc95bb9ca-04e8-4d54-9b70-24577a6dfac2/SBJ_seqcii_020.sv.vcf.gz as regions of interest
Sat Feb 6 02:46:27 UTC 2021: Using GRIDSS jar /usr/local/share/gridss-2.10.2-0/gridss.jar
Sat Feb 6 02:46:27 UTC 2021: Using output file seqcii_N020.slice.bam
Sat Feb 6 02:46:27 UTC 2021: Using 1 worker threads.
Sat Feb 6 02:46:27 UTC 2021: Found /tmp/tmp.Y5OiAo/gridsstools
Sat Feb 6 02:46:27 UTC 2021: Found /usr/local/bin/samtools
Sat Feb 6 02:46:27 UTC 2021: samtools version: 1.11
Using working directory "seqcii_N020.workingdir"
Sat Feb 6 02:46:27 UTC 2021: Converting SV VCF to BED of breakpoint positions.
Sat Feb 6 02:46:41 UTC 2021: Extending regions of interest by 5000 bp
Sat Feb 6 02:46:41 UTC 2021: Extracting reads of interest
[bed_read] Parse error reading "seqcii_N020.workingdir/tmp.seqcii_N020.slice.bam.gridss.target.bed" at line 1498 : end (5095) must not be less than start (18446744073709546616)
samtools view: Could not read file "seqcii_N020.workingdir/tmp.seqcii_N020.slice.bam.gridss.target.bed"
gridsstools: /usr/local/lib/libcurl.so.4: no version information available (required by gridsstools)
Read 0 distinct read names
The output bam file is then a mere 44Kb, which is very reduced compared to the 80Gb input.
Having looked at the tmp bed file, I noticed this at line 1498
chrY 3839333 3849398
chrY 14525467 14535878
chrY 14526088 14536091
chr17_KI270729v1_random 149952 160236
chr22_KI270738v1_random -5000 5095
chr22_KI270738v1_random 73930 84333
chrUn_KI270442v1 345931 356209
chrUn_KI270442v1 364970 375345
Could there be an issue with sv's very close to the chromosome start.
Having a look in the vcf file I have the following calls on this chromosome
##contig=<ID=chr22_KI270738v1_random,length=99375>
chr7 58057438 MantaBND:2:55316:55317:0:0:0:1 T T]chr22_KI270738v1_random:79132] . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:2:55316:55317:0:0:0:0;IMPRECISE;CIPOS=-175,176;SOMATIC;SOMATICSCORE=17;BND_DEPTH=81;MATE_BND_DEPTH=45 PR 45,1 114,7
chr22 16661931 MantaBND:88137:28:29:0:0:0:0 T [chr22_KI270738v1_random:48[T . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:88137:28:29:0:0:0:1;IMPRECISE;CIPOS=-154,154;SOMATIC;SOMATICSCORE=27;BND_DEPTH=56;MATE_BND_DEPTH=46 PR 37,0 73,5
chr22_KI270738v1_random 48 MantaBND:88137:28:29:0:0:0:1 T [chr22:16661931[T . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:88137:28:29:0:0:0:0;IMPRECISE;CIPOS=-47,47;SOMATIC;SOMATICSCORE=27;BND_DEPTH=46;MATE_BND_DEPTH=56 PR 37,0 73,5
chr22_KI270738v1_random 79132 MantaBND:2:55316:55317:0:0:0:0 A A]chr7:58057438] . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:2:55316:55317:0:0:0:1;IMPRECISE;CIPOS=-201,201;SOMATIC;SOMATICSCORE=17;BND_DEPTH=45;MATE_BND_DEPTH=81 PR 45,1 114,7
Alexis