Tophat2 Fail Bowtie2 align died

Question

[jhenderson]

I am new to NGS data analysis and using UC Davis Galaxy through AWS. I have RNA-Seq files that I checked by fastQC, ran through clip and sickle for quality and trimming, and then tried to align to hg19 and hg38 using tophat2 and have gotten the same error twice:

Fatal error: Tool execution failed

[2017-11-03 23:06:20] Beginning TopHat run (v2.1.0)
-----------------------------------------------
[2017-11-03 23:06:20] Checking for Bowtie
          Bowtie version:    2.2.3.0
[2017-11-03 23:06:20] Checking for Bowtie index files (genome)..
    Found both Bowtie1 and Bowtie2 indexes.
[2017-11-03 23:06:20] Checking for reference FASTA file
[2017-11-03 23:06:20] Generating SAM header for /data/refs/hg19/genome.fa
[2017-11-03 23:11:53] Preparing reads
     left reads: min. length=20, max. length=51, 21787476 kept reads (3274 discarded)
[2017-11-03 23:16:58] Mapping left_kept_reads to genome genome.fa with Bowtie2 
    [FAILED]
Error running bowtie:
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Error while flushing and closing output
terminate called recursively
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

Any advice/help would be great! I am not very familiar with a lot of computer language so layman's terms would be best. Thanks

[Kevin Blighe]

Do you have enough disk space under your account? Check with things like quota and df -h. Also try free -m for available RAM.

It will help just to check the exact command that you've also run.

[jared.andrews07]

Almost certainly seems like you're running out of memory, the signal 6 error (at least with bowtie) is one I've only run into when there's a memory issue. How many threads are you allotting to the program via the -p option? Are you running it on a cluster where you have to allocate memory to your job submission? If so, are you running it concurrently on multiple files?

Knowing the exact command and environment would help to answer these questions.