Are you using the latest version of samtools and HTSlib? If not, please specify.
(run samtools --version)
Please describe your environment.
- OS: Linux 5.15.0-1049-oracle
- machine architecture: x86_64
- compiler: gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
Using the attached aln.sam file:
samtools coverage --excl-flags 1540 aln.sam -o coverage.secondary.tsv
This gave a segmentation fault and produces a tsv output which stops part way through:
...
NOZR01000027.1 1 87550 1 109 0.1245 0.001245 53.9 0
NOZR01000030.1 1 70745 1 204 0.28836 0.0028836 61.7 0
NOZR01000039.1 1 35613 1 178 0.499817 0.00499817 66 0
NOZR01000054.1 1 5463 4 1072 19.6229 0.221856 61.3 0
NZ_RARC01000012.1 1 175888 1 47 0.0267216 0.000267216 50.6 0
NZ_RARC01000016.1 1 129040 2 167 0.129417 0.00129417 67.1 0
NZ_RARC0100002
The error occurs when samtools is installed via conda or installed from the github release. It runs fine if --excl-flags 1540 is removed.
Doing an initial debug it seems to be coming from here, but couldn't figure out beyond that:
Program received signal SIGSEGV, Segmentation fault.
0x0000555555593e43 in main_coverage (argc=argc@entry=6, argv=<optimised out>, argv@entry=0x7fffffffdc60) at coverage.c:614
614 bam_get_qual(p->b)[p->qpos] < opt_min_baseQ) --depth_at_pos; // low base quality
sam file came from mapping ont reads against an multifasta reference, which was then sorted.
minimap2 -ax map-ont --secondary yes -N 1000 ref.fa reads.fastq > alignments.sam
aln.zip
Are you using the latest version of samtools and HTSlib? If not, please specify.
(run
samtools --version)Please describe your environment.
Please specify the steps taken to generate the issue, the command you are running and the relevant output.
Using the attached aln.sam file:
This gave a segmentation fault and produces a tsv output which stops part way through:
The error occurs when samtools is installed via conda or installed from the github release. It runs fine if
--excl-flags 1540is removed.Doing an initial debug it seems to be coming from here, but couldn't figure out beyond that:
sam file came from mapping ont reads against an multifasta reference, which was then sorted.
aln.zip