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Old 01-07-2013, 07:53 AM   #1
magbju
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Default Tophat 2 error: Parse error at line 297359: missing colon in auxiliary data

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
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Old 01-10-2013, 02:22 AM   #2
magbju
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Location: Sweden

Join Date: Aug 2012
Posts: 4
Default

I reran the sample, and I am now receiving a different error (please see below). Could this be a tophat/bowtie bug?

[2013-01-09 17:59:01] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-01-09 17:59:01] Checking for Bowtie
Bowtie version: 2.0.4.0
[2013-01-09 17:59:01] Checking for Samtools
Samtools version: 0.1.18.0
[2013-01-09 17:59:01] Checking for Bowtie index files
[2013-01-09 17:59:01] Checking for reference FASTA file
[2013-01-09 17:59:01] Generating SAM header for /projects/NGS/bioDB/humanGenome/GRCh37_hg19/ensembl_annot/bowtie_ref/Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie
format: fastq
quality scale: phred33 (default)
[2013-01-09 17:59:09] 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)
[2013-01-09 18:20:49] Mapping left_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-09 18:53:36] Mapping left_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-09 18:56:55] Mapping left_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
[2013-01-09 18:59:49] Mapping right_kept_reads to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2
[2013-01-09 19:32:42] Mapping right_kept_reads_seg1 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (1/2)
[2013-01-09 19:36:15] Mapping right_kept_reads_seg2 to genome Homo_sapiens.GRCh37.68.dna.primary_assembly.bowtie with Bowtie2 (2/2)
Line 297360, sequence length 14 vs 25 from CIGAR
Parse error at line 297360: CIGAR and sequence length are inconsistent
[FAILED]
Error running bowtie:


gzip: stdout: Broken pipe
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Old 01-15-2013, 03:57 AM   #3
magbju
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Join Date: Aug 2012
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The solution was to upgrade to bowtie 2.0.5
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