Force Calling Errors

[ACEnglish]

Hello,

I'm attempting to run force calling from sniffles and are running into a few errors. The version I'm running is from develop (1e47c23)
Error 1:
When attempting to force call with command:

sniffles --input $bam --genotype-vcf $in_vcf --vcf output_genotypes.vcf -t 8

I get an error that

2024-04-02 12:14:18,855 ERROR sniffles.main (962219): Unhandled error while running sniffles.
Traceback (most recent call last):
  File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/bin/sniffles", line 514, in <module>
    Sniffles2_Main(processes)
  File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/bin/sniffles", line 444, in Sniffles2_Main
    t.result.emit(vcf_out=vcf_out, snf_out=snf_out)
  File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/lib/python3.10/site-packages/sniffles/result.py", line 50, in emit
    vcf_out.write_call(call)
  File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/lib/python3.10/site-packages/sniffles/vcf.py", line 159, in write_call
    for internal_id, sample_id in self.config.sample_ids_vcf:
AttributeError: 'SnifflesConfig' object has no attribute 'sample_ids_vcf'

A couple of more minor errors are:
Error 2- sniffles -h seems to throw an error. This is not a huge deal, just a small usability inconvience.

log.txt

!!!TRUNCATED FOR READABILITY BY ME!!! Usage example C - Determine genotypes for a set of known SVs (force calling): sniffles --input sample.bam --genotype-vcf input_known_svs.vcf --vcf output_genotypes.vcf

2024-04-02 12:06:09,811 ERROR sniffles.main (962157): Unhandled error while running sniffles.
Traceback (most recent call last):
File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/bin/sniffles", line 514, in
Sniffles2_Main(processes)
File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/bin/sniffles", line 70, in Sniffles2_Main
config = SnifflesConfig()
File "/stornext/snfs4/next-gen/scratch/english/round2/mpy/lib/python3.10/site-packages/sniffles/config.py", line 270, in init
parser.parse_args(args=args or None, namespace=self)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 1825, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 1858, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 2067, in _parse_known_args
start_index = consume_optional(start_index)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 2007, in consume_optional
take_action(action, args, option_string)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 1935, in take_action
action(self, namespace, argument_values, option_string)
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 1099, in call
parser.exit()
File "/hgsc_software/python/python-3.10.4/lib/python3.10/argparse.py", line 2569, in exit
_sys.exit(status)
SystemExit: 0

Error 3 - Another minor inconvenience is that if the --genotype-vcf does not exist, an uniformative error is thrown.

log.txt

2024-04-02 12:06:17,170 INFO sniffles.main (962160): Running Sniffles2, build 2.3.0-rc2 2024-04-02 12:06:17,170 INFO sniffles.main (962160): Run Mode: genotype_vcf 2024-04-02 12:06:17,170 INFO sniffles.main (962160): Start on: 2024/04/02 12:06:17 2024-04-02 12:06:17,170 INFO sniffles.main (962160): Working dir: /stornext/snfs4/next-gen/scratch/english/round2/aou_sv_merge/genotyping/sniffles/giab_HG002 2024-04-02 12:06:17,170 INFO sniffles.main (962160): Used command: /stornext/snfs4/next-gen/scratch/english/round2/mpy/bin/sniffles --input /stornext/snfs4/next-gen/scratch/medhat/projects/HGSC_SUmmit_2023/PacBio_Movie_24_vs_30_2024-01-11/movie_24/analysis_38/result/HG002_24h.minimap.hap.bam --genotype-vcf /users/u233287/scratch/aou_sv_merge/genotyping/kanpig/giab_HG002/custom_giabv1.0/GIABv1.0.vcf.gz --vcf output_genotypes.vcf -t 8 2024-04-02 12:06:17,170 INFO sniffles.main (962160): ============================== 2024-04-02 12:06:17,170 INFO sniffles.resources (962160): Logging memory usage to None 2024-04-02 12:06:17,170 INFO sniffles.main (962160): Opening for reading: /stornext/snfs4/next-gen/scratch/medhat/projects/HGSC_SUmmit_2023/PacBio_Movie_24_vs_30_2024-01-11/movie_24/analysis_38/result/HG002_24h.minimap.hap.bam cmd.sh: line 13: 962160 Segmentation fault (core dumped) sniffles --input $bam --genotype-vcf $in_vcf --vcf output_genotypes.vcf -t 8

real 0m0.837s
user 0m0.253s
sys 0m0.091s

[hermannromanek]

Hi Adam,

Thanks for testing & reporting, I'll fix them as soon as possible.

Hermann

[hermannromanek]

Hi Adam,

I just pushed fixes for the first two issues. The third one seems to be the result of using an internal class of pysam. I think the best way to fix that is to change the usage to documented classes which (in my brief test) handle a missing file gracefully by raising an exception instead of killing the process by segfault. I'll add that to the To-Do-List for v2.4.

Thanks,
Hermann