Aborted core dumped error

[pcantalupo]

Hello,

I ran Squid v1.5 using 12 cpus and 96 GB RAM with the following command:

squid -b AUR1.Aligned.sortedByCoord.out.bam -c AUR1_chimeric_sorted.bam -o AUR1.squid.fusions

Here is the output and it was aborted because of a core dump

Reference name 1    --> 0
Reference name 10   --> 1
Reference name 11   --> 2
Reference name 12   --> 3
Reference name 13   --> 4
Reference name 14   --> 5
Reference name 15   --> 6
Reference name 16   --> 7
Reference name 17   --> 8
Reference name 18   --> 9
Reference name 19   --> 10
Reference name 2    --> 11
Reference name 20   --> 12
Reference name 21   --> 13
Reference name 22   --> 14
Reference name 3    --> 15
Reference name 4    --> 16
Reference name 5    --> 17
Reference name 6    --> 18
Reference name 7    --> 19
Reference name 8    --> 20
Reference name 9    --> 21
Reference name MT   --> 22
Reference name X    --> 23
Reference name Y    --> 24
[Tue Dec 27 10:30:53 2022] Start reading bam file.
[Tue Dec 27 10:31:03 2022] Finish sorting Chimeric bam reads.
[Tue Dec 27 10:31:05 2022] Finish removing PCR duplicates.
[Tue Dec 27 10:31:07 2022] Building nodes. |bamdiscordant|=3076123
[Tue Dec 27 10:42:51 2022] Building nodes, finish seeding.
[Tue Dec 27 10:42:51 2022] Building nodes, finish expanding to whole genome.
[Tue Dec 27 10:42:51 2022] Building nodes, calculating read coverage for node 0.
[Tue Dec 27 10:42:52 2022] Finish calculating reads per node.
0   time=7e-06
1000000 time=17.1684
[Tue Dec 27 10:43:20 2022] Starting building edges.
[Tue Dec 27 10:51:54 2022] Finish raw edges.
[Tue Dec 27 10:51:54 2022] Finish filtering edges from multi-aligned reads.
[Tue Dec 27 10:51:55 2022] Finish building edges.
Maximum connected component size=2469
6525    10137
glp_add_rows: nrs = 1; too many rows
Error detected in file api/prob1.c at line 259
run.sh: line 2: 79383 Aborted                 (core dumped) squid -b AUR1.Aligned.sortedByCoord.out.bam -c AUR1_chimeric_sorted.bam -o AUR1.squid.fusions

Following Issue https://github.com/Kingsford-Group/squid/issues/4#issuecomment-395808438, I get no output from the following command so that means there are no reads with only the first read or second read aligned. /usr/bin/diff <(samtools view -f64 -F4 AUR1_chimeric_sorted.bam | cut -f1 | sort | uniq) <(samtools view -f128 -F4 AUR1_chimeric_sorted.bam | cut -f1 | sort | uniq)

Here is the header from the Chimeric bam file so you can see the commands used to generate it:

@PG     ID:STAR PN:STAR VN:2.7.10a      CL:STAR   --runThreadN 12   --genomeDir star   --readFilesIn AUR1_S7_L004_R1_001.fastq.gz   AUR1_S7_L004_R2_001.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix AUR1.   --outReadsUnmapped Fastx   --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField intronMotif   --outSAMattrRGline ID:AUR1   SM:AUR1      --alignSJDBoverhangMin 10   --chimSegmentMin 20   --chimJunctionOverhangMin 12   --chimOutType SeparateSAMold      --sjdbGTFfile Homo_sapiens.GRCh38.102.gtf   --twopassMode Basic
@PG     ID:samtools     PN:samtools     PP:STAR VN:1.15.1       CL:samtools view --threads 5 -Sb -o AUR1_chimeric.bam AUR1.Chimeric.out.sam
@PG     ID:samtools.1   PN:samtools     PP:samtools     VN:1.15.1       CL:samtools sort -@ 6 -o AUR1_chimeric_sorted.bam -T AUR1_chimeric_sorted AUR1_chimeric.bam
@PG     ID:samtools.2   PN:samtools     PP:samtools.1   VN:1.14 CL:samtools view -H AUR1_chimeric_sorted.bam
@RG     ID:AUR1 SM:AUR1
@CO     user command line: STAR --genomeDir star --readFilesIn AUR1_S7_L004_R1_001.fastq.gz AUR1_S7_L004_R2_001.fastq.gz --runThreadN 12 --outFileNamePrefix AUR1. --sjdbGTFfile Homo_sapiens.GRCh38.102.gtf --outSAMattrRGline ID:AUR1 SM:AUR1 --twopassMode Basic --chimOutType SeparateSAMold --chimSegmentMin 20 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --outReadsUnmapped Fastx --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat

I tried the same command on a different system and got a similar error except it was reported as a Segmentation fault.

What could be causing the problem? Thank you

[MikeWLloyd]

Seeing this exact error, did you ever figure it out?

[pcantalupo]

Seeing this exact error, did you ever figure it out?

Unfortunately no.