Hi,
this is the first time I run Tophat, and I cannot get it to work.
I have two test fastq files, each one containing 10 reads. They align well to hg19 with bowtie:
However, tophat complains:
I get the following output, again and again with different settings:
If anyone knows what is going on, I would be so thankful...
this is the first time I run Tophat, and I cannot get it to work.
I have two test fastq files, each one containing 10 reads. They align well to hg19 with bowtie:
bowtie --phred64-quals indexes/h_sapiens_37_asm -1 test_1.fastq -2 test_2.fastq
# reads processed: 10
# reads with at least one reported alignment: 5 (50.00%)
# reads that failed to align: 5 (50.00%)
Reported 5 paired-end alignments to 1 output stream(s)
# reads processed: 10
# reads with at least one reported alignment: 5 (50.00%)
# reads that failed to align: 5 (50.00%)
Reported 5 paired-end alignments to 1 output stream(s)
However, tophat complains:
tophat --keep-tmp -r 15 -o test --phred64-quals indexes/h_sapiens_37_asm test_1.fastq test_2.fastq
[Tue Jul 12 15:06:45 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Tue Jul 12 15:06:45 2011] Preparing output location test/
[Tue Jul 12 15:06:45 2011] Checking for Bowtie index files
[Tue Jul 12 15:06:45 2011] Checking for reference FASTA file
[Tue Jul 12 15:06:45 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jul 12 15:06:45 2011] Checking for Samtools
Samtools Version: 0.1.15
[Tue Jul 12 15:06:45 2011] Generating SAM header for indexes/h_sapiens_37_asm
[Tue Jul 12 15:06:48 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
Left reads: min. length=53, count=10
Right reads: min. length=53, count=10
[Tue Jul 12 15:06:48 2011] Mapping left_kept_reads against h_sapiens_37_asm with Bowtie
[FAILED]
Error at mkfifo(test/tmp/31660.bwt_unmapped.z.fifo). [Errno 5] Input/output error
-----------------------------------------------
[Tue Jul 12 15:06:45 2011] Preparing output location test/
[Tue Jul 12 15:06:45 2011] Checking for Bowtie index files
[Tue Jul 12 15:06:45 2011] Checking for reference FASTA file
[Tue Jul 12 15:06:45 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jul 12 15:06:45 2011] Checking for Samtools
Samtools Version: 0.1.15
[Tue Jul 12 15:06:45 2011] Generating SAM header for indexes/h_sapiens_37_asm
[Tue Jul 12 15:06:48 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
Left reads: min. length=53, count=10
Right reads: min. length=53, count=10
[Tue Jul 12 15:06:48 2011] Mapping left_kept_reads against h_sapiens_37_asm with Bowtie
[FAILED]
Error at mkfifo(test/tmp/31660.bwt_unmapped.z.fifo). [Errno 5] Input/output error
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