Hi,
I am getting the following error for one of my samples processed using tophat 2.0.6 (16 out of 17 samples worked fine), has anyone else seen something similar? The right_kept_reads_seg2.bam and right_kept_reads_seg2_unmapped.bam are small (1.7KB) and the corresponding samtools index files are empty. It may be a Samtools error, however, I cannot seem to find the root cause.
Many thanks!
Magnus
[2013-01-07 14:14:05] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-01-07 14:14:05] Checking for Bowtie
Bowtie version: 2.0.4.0
[2013-01-07 14:14:05] Checking for Samtools
Samtools version: 0.1.18.0
[2013-01-07 14:14:05] Checking for Bowtie index files
[2013-01-07 14:14:05] Checking for reference FASTA file
[2013-01-07 14:14:05] Generating SAM header for .../bowtie_ref/Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie
format: fastq
quality scale: phred33 (default)
[2013-01-07 14:14:13] Preparing reads
left reads: min. length=20, max. length=50, 52792789 kept reads (3856 discarded)
right reads: min. length=20, max. length=50, 52791358 kept reads (5287 discarded)
[2013-01-07 14:35:55] Mapping left_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-07 15:08:43] Mapping left_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-07 15:12:00] Mapping left_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
[2013-01-07 15:14:55] Mapping right_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-07 15:47:50] Mapping right_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-07 15:51:25] Mapping right_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
Parse error at line 297359: missing colon in auxiliary data
[FAILED]
Error running bowtie:
gzip: stdout: Broken pipe
I am getting the following error for one of my samples processed using tophat 2.0.6 (16 out of 17 samples worked fine), has anyone else seen something similar? The right_kept_reads_seg2.bam and right_kept_reads_seg2_unmapped.bam are small (1.7KB) and the corresponding samtools index files are empty. It may be a Samtools error, however, I cannot seem to find the root cause.
Many thanks!
Magnus
[2013-01-07 14:14:05] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-01-07 14:14:05] Checking for Bowtie
Bowtie version: 2.0.4.0
[2013-01-07 14:14:05] Checking for Samtools
Samtools version: 0.1.18.0
[2013-01-07 14:14:05] Checking for Bowtie index files
[2013-01-07 14:14:05] Checking for reference FASTA file
[2013-01-07 14:14:05] Generating SAM header for .../bowtie_ref/Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie
format: fastq
quality scale: phred33 (default)
[2013-01-07 14:14:13] Preparing reads
left reads: min. length=20, max. length=50, 52792789 kept reads (3856 discarded)
right reads: min. length=20, max. length=50, 52791358 kept reads (5287 discarded)
[2013-01-07 14:35:55] Mapping left_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-07 15:08:43] Mapping left_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-07 15:12:00] Mapping left_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
[2013-01-07 15:14:55] Mapping right_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-07 15:47:50] Mapping right_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-07 15:51:25] Mapping right_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
Parse error at line 297359: missing colon in auxiliary data
[FAILED]
Error running bowtie:
gzip: stdout: Broken pipe
Comment