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Kingsford-Group
Aborted core dumped error
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
