Bowtie2-align died with signal 24 (XCPU)

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Alex Glathar

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Aug 18, 2019, 2:48:02 PM8/18/19

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I am trying to run TopHat, but keep running into this error no matter which version of TopHat or BowTie I use. Any insight into his issue is appreciated. ______________________________________________________________________________________________________________________________________________________________

[2019-08-18 14:30:33] Beginning TopHat run (v2.0.13)

-----------------------------------------------

[2019-08-18 14:30:33] Checking for Bowtie

Bowtie version: 2.2.6.0

[2019-08-18 14:30:33] Checking for Bowtie index files (genome)..

[2019-08-18 14:30:33] Checking for reference FASTA file

[2019-08-18 14:30:33] Generating SAM header for /projects/academic/mjbuck/References/igenome-041714/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome

[2019-08-18 14:30:35] Reading known junctions from GTF file

[2019-08-18 14:30:38] Preparing reads

left reads: min. length=51, max. length=51, 31818432 kept reads (2484 discarded)

[2019-08-18 14:33:38] Building transcriptome data files /projects/academic/mjbuck/Collaborators/Sinha_Core_File_Deposit/Alex_safe_Zone/Mouse_Cell_Lines/all_bams//tmp/genes

[2019-08-18 14:33:48] Building Bowtie index from genes.fa

[2019-08-18 14:40:35] Mapping left_kept_reads to transcriptome genes with Bowtie2

[FAILED]

Error running bowtie:

(ERR): bowtie2-align died with signal 24 (XCPU)

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