Segmentation fault with centromere annotation for bias detection

[baozg]

Hi, @mobinasri

I am running hmm-flagger with bias detection as we could saw overall twice coverage in centromere region. But hmm_flagger end up with segementaion fault. Could you help me check which step may have problem?

Command:

echo "{" > ${prefix}_annotations_path.json
echo \"whole_genome\" : \"/data/${prefix}.wg.bed\", >> ${prefix}_annotations_path.json
echo \"centromere\" : \"/data/${prefix}.centromere.bed\" >> ${prefix}_annotations_path.json
echo "}" >> ${prefix}_annotations_path.json
singularity run -B ${PWD}:/data/ /ebio/abt6_projects/AtGraph/conda/software/flagger/flagger-1.0.0.sif \
  bam2cov --bam /data/${BAM_FILE} \
                  --output /data/${prefix}_coverage_file.cov.gz \
                  --threads 16 \
                  --runBiasDetection \
                  --annotationJson /data/${prefix}_annotations_path.json \
                  --baselineAnnotation whole_genome

mkdir -p ${prefix}_hmm_flagger_output
singularity run -B ${PWD}:/data/ /ebio/abt6_projects/AtGraph/conda/software/flagger/flagger-1.0.0.sif \
    hmm_flagger \
            --input /data/${prefix}_coverage_file.cov.gz \
            --outputDir /data/${prefix}_hmm_flagger_output  \
            --alphaTsv /home/programs/config/alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv \
            --labelNames Err,Dup,Hap,Col \
            --threads 5

log:

[2024-11-05 18:20:53] Created block table for whole genome  : tot_len=134371593, number=5
{
"whole_genome" : "/data/Col-0_LZU.wg.bed",
"centromere" : "/data/Col-0_LZU.centromere.bed"
}
[2024-11-05 18:20:53] Parsed  annotation whole_genome:/data/Col-0_LZU.wg.bed
[2024-11-05 18:20:53] Parsed  annotation centromere:/data/Col-0_LZU.centromere.bed
[2024-11-05 18:20:53] Number of created annotation block tables = 3
[2024-11-05 18:20:53] Added annotation blocks to coverage block tables: tot_len=415189086, number=394047
[2024-11-05 18:20:53] Started sorting and merging blocks
[2024-11-05 18:20:53] Blocks before merging : tot_len=415189086, number=394047
[2024-11-05 18:20:53] Created final block table : tot_len=134371593, number=402195
{
"whole_genome" : "/data/Col-0_LZU.wg.bed",
"centromere" : "/data/Col-0_LZU.centromere.bed"
}
[2024-11-05 18:20:53] Number of annotations added to the blocks table (+1 for 'no_annotation' which is a reserved annotation name for blocks with no annotation): 3
[2024-11-05 18:20:53] --restrictBiasAnnotations is not provided so all annotations will be checked for coverage bias!
[2024-11-05 18:20:53] Writing coverage bias table into this file /data/Col-0_LZU_coverage_file.bias_detection_table.tsv
[2024-11-05 18:20:53] Started writing to /data/Col-0_LZU_coverage_file.cov.gz.
[2024-11-05 18:20:55] Done.
Real time: 39.737 sec; CPU: 134.994 sec; Peak RSS: 0.197 GB; CPU usage: 339.7%
INFO:    Cleaning up image...
INFO:    Converting SIF file to temporary sandbox...
[2024-11-05 18:21:13] Parsing/Creating coverage chunks.
[2024-11-05 18:21:13] The given input file is not binary so chunks will be constructed from cov file.
[2024-11-05 18:21:13] Index file exists: /data/Col-0_LZU_coverage_file.cov.gz.index
[2024-11-05 18:21:13] Parsing index ...
[2024-11-05 18:21:13] Index is parsed from disk.
[2024-11-05 18:21:13] Parsing header info for ChunksCreator.
[2024-11-05 18:21:13] Truth tag was set to false (or not defined) so truth labels will not be parsed from file.
[2024-11-05 18:21:13] Prediction tag was set to false (or not defined) so prediction labels will not be parsed from file.
[2024-11-05 18:21:13] Creating empty chunks.
[2024-11-05 18:21:13] Created a thread pool with 5 threads for parsing chunks
[2024-11-05 18:21:13] Queued 5 jobs for the thread pool (no more than 5 jobs will be processed at a time)
INFO:    Cleaning up image...
run.sh: line 43: 111753 Segmentation fault      singularity run -B ${PWD}:/data/ /ebio/abt6_projects/AtGraph/conda/software/flagger/flagger-1.0.0.sif hmm_flagger --input /data/${prefix}_coverage_file.cov.gz --outputDir /data/${prefix}_hmm_flagger_output --alphaTsv /home/programs/config/alpha_optimum_trunc_exp_gaussian_w_4000_n_50.tsv --labelNames Err,Dup,Hap,Col --threads 5

[mobinasri]

@baozg Thanks for reporting this. It is not obvious to me what is worng.
Can you test flagger-v1.1? If you could provide the cov.gz file and those bed files I can test it on my side as well.