Hey guys I'm getting this error with Tophat and I can't seem to figure out why, I'm using paired end reads from Illumina HiSeq. Any tips? I figured it might just be one read thats the problem so I removed it but then I got another one.
[2012-11-21 16:45:33] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-11-21 16:45:33] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-11-21 16:45:33] Checking for Samtools
Samtools version: 0.1.18.0
[2012-11-21 16:45:33] Checking for Bowtie index files
[2012-11-21 16:45:33] Checking for reference FASTA file
Warning: Could not find FASTA file hg19.fa
[2012-11-21 16:45:33] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bowtie2/bowtie2-inspect hg19 > ./tophat_out/tmp/hg19.fa
[2012-11-21 16:48:12] Generating SAM header for hg19
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2012-11-21 16:49:04] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)
[2012-11-21 16:45:33] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-11-21 16:45:33] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-11-21 16:45:33] Checking for Samtools
Samtools version: 0.1.18.0
[2012-11-21 16:45:33] Checking for Bowtie index files
[2012-11-21 16:45:33] Checking for reference FASTA file
Warning: Could not find FASTA file hg19.fa
[2012-11-21 16:45:33] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/local/bowtie2/bowtie2-inspect hg19 > ./tophat_out/tmp/hg19.fa
[2012-11-21 16:48:12] Generating SAM header for hg19
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2012-11-21 16:49:04] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: read #1 (HWI-ST993:228:C0RWJACXX:6:2316:17166:97507) does not have a matching mate in the same order (HWI-ST993:228:C0RWJACXX:6:2316:12084:97378 found instead)
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