ERROR on tophat: Mapping left_kept_reads to genome Athaliana with Bowtie2

Question

[catherine]

I kept get this error when running tophat. Can anyone help me with it?

Thank you very much!!!

My command is

tophat2 -I 12000 -i 70 -o SRR797194 -p 12 Athaliana SRR797194.fastq

and the error I got is

[2015-02-24 22:02:13] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2015-02-24 22:02:14] Checking for Bowtie
                  Bowtie version:        2.2.3.0
[2015-02-24 22:02:14] Checking for Samtools
                Samtools version:        0.1.19.0
[2015-02-24 22:02:14] Checking for Bowtie index files (genome)..
[2015-02-24 22:02:14] Checking for reference FASTA file
[2015-02-24 22:02:14] Generating SAM header for Athaliana
[2015-02-24 22:02:14] Preparing reads
         left reads: min. length=50, max. length=50, 2260990 kept reads (2 discarded)
[2015-02-24 22:02:35] Mapping left_kept_reads to genome Athaliana with Bowtie2 
        [FAILED]
Error running bowtie:
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
Error while flushing and closing output
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT)

[Devon Ryan]

Typically the only way to diagnose this problem is by looking in the run log and manually executing the last command in there. You'll then hopefully get a more informative error message. However, first check to ensure that there's room on the hard drive. Perhaps it's full.

[catherine]

I run it in cluster, so I don't think its ram problem...(I set 24gb to run one 1gb-fastq file)

Answer 1

[iraun]

I suggest you to read these two threads related with your problem:

• http://seqanswers.com/forums/showthread.php?t=15599
• https://groups.google.com/forum/#!msg/tuxedo-tools-users/vG5Rn0IgxoA/plOE89Yi55kJ

Most probably, the problem is that your machine ran out of RAM.

Hope it helps.

[catherine]

I run it in cluster, so I don't think its ram problem...(I set 24gb to run one 1gb-fastq file)

Answer 2

[catherine]

I solved it by changing the version of bowtie. I was using bowtie2/intel/2.2.3, then after changing it to bowtie2/intel/2.2.1, it works.