Segmentation fault with hmm_flagger

[jkfo002]

Hi, @mobinasri

I am running flagger v1.2 with singularity container, but end up with hmm_flagger segementaion fault. Could you help me what happened here ?

Command

singularity=~/00_biosoft/singularity-ce-3.10.3/bin/singularity
flagger=~/00_biosoft/

cat hap1.fa hap2.fa > hapall.fa
seqkit sort -nN hapall.fa > hapall_sorted.fa
samtools faidx hapall_sorted.fa
cat hapall_sorted.fa.fai | awk '{print $1"\t0\t"$2}' > whole_genome.bed

minimap2 -t 20 -ax map-hifi -k 21 hapall_sorted.fa hifi.fa | samtools view -hb | samtools sort - > 334_sorted.bam
samtools index 334_sorted.bam

# Convert BAM to COV
echo "{" > annotations_path.json
echo \"whole_genome\" : \"${PWD}/whole_genome.bed\" >> annotations_path.json
echo "}" >> annotations_path.json
singularity exec -B 'pwd' flagger_v1.2.sif \
bam2cov --bam 334_sorted.bam \
--output coverage_file.cov.gz \
--annotationJson annotations_path.json \
--threads 16 \
--baselineAnnotation whole_genome

# hmm_flagger
mkdir -p hmm_flagger_outputs
singularity exec -B 'pwd' flagger_v1.2.sif \
hmm_flagger --input coverage_file.cov.gz \
--outputDir hmm_flagger_outputs  \
--alphaTsv /home/programs/config/alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv \
--labelNames Err,Dup,Hap,Col \
--threads 16

log

{
"whole_genome" : "/public/agis/huangsanwen_group/daijichen/01_run/flagger/334/whole_genome.bed"
}
[2025-01-06 18:56:04] Parsed annotation whole_genome:/public/agis/huangsanwen_group/daijichen/01_run/flagger/334/whole_genome.bed
[2025-01-06 18:56:04] Number of created annotation block tables = 2
[2025-01-06 18:56:04] Added annotation blocks to coverage block tables: tot_len=4519929413, number=10540557
[2025-01-06 18:56:04] Started sorting and merging blocks
[2025-01-06 18:56:06] Blocks before merging : tot_len=4519929413, number=10540557
[2025-01-06 18:56:07] Created final block table : tot_len=1506657645, number=10540563
{
"whole_genome" : "/public/agis/huangsanwen_group/daijichen/01_run/flagger/334/whole_genome.bed"
}
[2025-01-06 18:56:08] Number of annotations added to the blocks table (+1 for 'no_annotation' which is a reserved annotation name for blocks with no annotation): 2
[2025-01-06 18:56:08] Bias detection is disabled. Running bias module only for getting the whole genome median coverage.
[2025-01-06 18:56:09] Whole genome median coverage = 62
[2025-01-06 18:56:18] Started writing to coverage_file.cov.gz.
[2025-01-06 18:56:46] Done.
Real time: 362.365 sec; CPU: 1593.146 sec; Peak RSS: 4.666 GB; CPU usage: 439.7%
INFO: Cleaning up image...
INFO: Converting SIF file to temporary sandbox...
[2025-01-06 18:57:03] Parsing/Creating coverage chunks.
[2025-01-06 18:57:03] The given input file is not binary so chunks will be constructed from cov file.
[2025-01-06 18:57:03] Index file does not exist: expected path coverage_file.cov.gz.index
[2025-01-06 18:57:03] Constructing index in memory ...
[2025-01-06 18:57:15] Index is constructed.
[2025-01-06 18:57:15] Index file (coverage_file.cov.gz.index) is written
[2025-01-06 18:57:15] Index is saved into coverage_file.cov.gz.index (It will skip index construction for next runs).
[2025-01-06 18:57:15] Parsing header info for ChunksCreator.
[2025-01-06 18:57:18] Truth tag was set to false (or not defined) so truth labels will not be parsed from file.
[2025-01-06 18:57:18] Prediction tag was set to false (or not defined) so prediction labels will not be parsed from file.
[2025-01-06 18:57:18] Creating empty chunks.
[2025-01-06 18:57:18] Created a thread pool with 10 threads for parsing chunks
[2025-01-06 18:57:18] Queued 64 jobs for the thread pool (no more than 10 jobs will be processed at a time)
[2025-01-06 18:58:31] Chunks are constructed from cov file.
[2025-01-06 18:58:31] 64 chunks are parsed covering total length of 1506657645 bases.
[2025-01-06 18:58:31] Determining the number of components for the 'collapsed' state.
[2025-01-06 18:58:31] The number of collapsed components (n=5) is determined and adjusted automatically by taking the maximum observed coverage.
[2025-01-06 18:58:31] Creating HMM model.
INFO: Cleaning up image...
/var/spool/slurm/d/job17358112/slurm_script: line 111: 32694 Segmentation fault (core dumped) $singularity exec -B pwd $flagger hmm_flagger --input coverage_file.cov.gz --outputDir hmm_flagger_outputs --alphaTsv /home/programs/config/alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv --labelNames Err,Dup,Hap,Col --threads 10

Coverge file
coverage_file.cov.head10000.gz

[mobinasri]

@jkfo002 Are you using mobinasri/flagger:v1.2.0-dev this is still in development. your coverage file looked fine to me. Could you please provide the full coverage file?

[jkfo002]

Sure, please check https://drive.google.com/file/d/1wN03g8eIkjbp2kd8KGNaEdVV4chjnJtx/view?usp=drive_link

[mobinasri]

Thanks @jkfo002 it seems that the link is not public. I just asked you to give permission.

[jkfo002]

Sorry @mobinasri, please check again whether the link accessible.