Segmentation fault (core dumped)

[timedreamer]

Hi,

My SQUID run returned this error. Any ideas?

squid -b SRR3138207Aligned.sortedByCoord.out.bam -c SRR3138207Chimeric.out.bam -o squidout

Return:

[Thu Apr 19 16:13:22 2018] Start reading bam file.
[Thu Apr 19 16:14:03 2018] Finish sorting Chimeric bam reads.
[Thu Apr 19 16:14:05 2018] Finish removing PCR duplicates.
[Thu Apr 19 16:14:08 2018] Building nodes. |bamdiscordant|=1519417
[Thu Apr 19 16:32:12 2018] Building nodes, finish seeding.
[Thu Apr 19 16:32:12 2018] Building nodes, finish expanding to whole genome.
[Thu Apr 19 16:32:12 2018] Building nodes, calculating read coverage for node 0.
[Thu Apr 19 16:32:23 2018] Finish calculating reads per node.
0       time=0.001708
[Thu Apr 19 16:36:21 2018] Starting building edges.
Segmentation fault (core dumped)

Many thanks.

Ji

[Congm12]

Could you share your bam files?

[timedreamer]

Sure. Here is the google drive link for the two bam files.

The STAR command I used is this:

STAR --genomeDir {STARREF} --readFilesCommand zcat \
        --readFilesIn {input.r1} {input.r2} \
        --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 \
        --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 10 \
        --quantMode GeneCounts --outReadsUnmapped None --outSAMstrandField intronMotif \
        --chimOutType SeparateSAMold --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 \
        --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax 3\
        -alignSJstitchMismatchNmax 5 -1 5 5 \
        --runThreadN {threads} --outFileNamePrefix '../data/star_output/{wildcards.sample}'

Thanks for your time!

[Congm12]

The latest release should fix that error. Please check out to see whether the latest version works, or whether there are new problems.

[timedreamer]

Works fine now. Thanks!