Hello all,
TopHat crashes on my files after apparently aligning reads with bowtie for some time.
Here is the error message:
####
foobar$ tophat -p 8 -o TOPHAT /refgenome/hg19 Sample1.fastq
[2013-02-01 17:15:03] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-01 17:15:03] Checking for Bowtie
Bowtie version: 2.0.4.0
[2013-02-01 17:15:03] Checking for Samtools
Samtools version: 0.1.18.0
Warning: we do not recommend to have both Bowtie1 and Bowtie2 indexes in the same directory
the genome sequence (*.fa) may not be compatible with one of them
[2013-02-01 17:15:03] Checking for reference FASTA file
format: fastq
quality scale: phred33 (default)
[2013-02-01 17:15:03] Preparing reads
left reads: min. length=202, max. length=202, 415678243 kept reads (42823 discarded)
[2013-02-01 23:07:52] Mapping left_kept_reads to genome hg19 with Bowtie2
[FAILED]
Error running bowtie:
foobar$
####
As you can see, the error message is not terribly informative regarding the nature of the problem.
Mysteriously, I am able to get TopHat to run just fine on a smaller file consisting of the first 100,000 reads of that same fastq file.
So it IS able to run fine given my current setup, just not on the full size file which granted is quite large...might this be the issue?
If anyone has any insight into this issue, I would greatly appreciate your thoughts and expertise.
Best regards,
Batool
TopHat crashes on my files after apparently aligning reads with bowtie for some time.
Here is the error message:
####
foobar$ tophat -p 8 -o TOPHAT /refgenome/hg19 Sample1.fastq
[2013-02-01 17:15:03] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-02-01 17:15:03] Checking for Bowtie
Bowtie version: 2.0.4.0
[2013-02-01 17:15:03] Checking for Samtools
Samtools version: 0.1.18.0
Warning: we do not recommend to have both Bowtie1 and Bowtie2 indexes in the same directory
the genome sequence (*.fa) may not be compatible with one of them
[2013-02-01 17:15:03] Checking for reference FASTA file
format: fastq
quality scale: phred33 (default)
[2013-02-01 17:15:03] Preparing reads
left reads: min. length=202, max. length=202, 415678243 kept reads (42823 discarded)
[2013-02-01 23:07:52] Mapping left_kept_reads to genome hg19 with Bowtie2
[FAILED]
Error running bowtie:
foobar$
####
As you can see, the error message is not terribly informative regarding the nature of the problem.
Mysteriously, I am able to get TopHat to run just fine on a smaller file consisting of the first 100,000 reads of that same fastq file.
So it IS able to run fine given my current setup, just not on the full size file which granted is quite large...might this be the issue?
If anyone has any insight into this issue, I would greatly appreciate your thoughts and expertise.
Best regards,
Batool
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