System.Error::Signal raised (no=11) using bs_call

[dy-lin]

With this command, I'm encountering an error:

/usr/local/anaconda/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call -r /ref/hg38_no_alt.gemBS.ref \
    -n TGACCA \
    --contig-bed /out_dir///calls/TGACCA/contigs_TGACCA_chr4.bed \
    --contig-sizes /ref/hg38_no_alt.contig.sizes \
    --report-file /out_dir///calls/TGACCA/TGACCA_chr4.json \
    --right-trim 0 \
    --left-trim 0 \
    -k \
    --conversion 0.0237,0.0500 \
    --reference-bias 2 \
    --mapq-threshold 10 \
    --bq-threshold 13 \
    -t 16 \
    -O b \
    -o /out_dir///calls/TGACCA/TGACCA_chr4.bcf \
    /out_dir///mapping/TGACCA/TGACCA.bam

Additional threads:  7 4 5
Loading reference sequence index
Sequence index read in successfully
Opened /out_dir///mapping/TGGCGC/TGGCGC.bam for input (Index)
Processing region chr4:1-190214555
Processing chromosome chr4 (OK)
Loading reference for chr4
len = 190214555
Read in 190204555 bases on chr4 from 10001 - 190214555, stored in 76081824 bytes
> System.Error::Signal raised (no=11)

Are there any other log files generated where I can troubleshoot the origin of this System.Error::Signal raised (no=11) error?

[dy-lin]

I've since noticed that while this is in the log file, the invoked command was gemBS call.

[heathsc]

Dear Diana,

Would it be possible to get a small dataset that you could share that reliably causes this crash?

Yours, Simon

On Fri, Dec 2, 2022 at 12:37 AM Diana Lin @.***> wrote:

I've since noticed that while this is in the log file, the invoked command was gemBS call.

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