Dear community,
I have a problem with prep_reads running TopHat2, like so many other. I have looked at all previous threads, and that solved my problem only partly.
I had 12 multiplexed RNA samples that I ran on 6 lanes on an Illumina HiSeq2000. After retrieving the data I made a custom program to demultiplex the samples and combine the data from the 6 lanes. On the resulting fastq files I tried to run TopHat. First I used:
/tophat/tophat2 -o TophatOutput_sample -p 4 /Bowtie2index/hg19 sample.fq
That worked for 8 out of 12 samples. After reading a bit on this forum I realized that I had phred quality score 64, so I added --solexa1.3-quals. That solved the issue for another three samples, but still I cannot run TopHat on the last sample. I receive the following error message for that sample:
[2013-05-28 22:02:25] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2013-05-28 22:02:25] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-05-28 22:02:25] Checking for Samtools
Samtools version: 0.1.9.0
[2013-05-28 22:02:25] Checking for Bowtie index files
[2013-05-28 22:02:25] Checking for reference FASTA file
[2013-05-28 22:02:25] Generating SAM header for /data/genomes/hg19/genome/Bowtie2index/hg19
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2013-05-28 22:02:30] Preparing reads
[FAILED]
Error running 'prep_reads'
---------------------------
My prep_reads.log is empty.
I would be very happy if anyone could tell me how to solve the problem!
I have a problem with prep_reads running TopHat2, like so many other. I have looked at all previous threads, and that solved my problem only partly.
I had 12 multiplexed RNA samples that I ran on 6 lanes on an Illumina HiSeq2000. After retrieving the data I made a custom program to demultiplex the samples and combine the data from the 6 lanes. On the resulting fastq files I tried to run TopHat. First I used:
/tophat/tophat2 -o TophatOutput_sample -p 4 /Bowtie2index/hg19 sample.fq
That worked for 8 out of 12 samples. After reading a bit on this forum I realized that I had phred quality score 64, so I added --solexa1.3-quals. That solved the issue for another three samples, but still I cannot run TopHat on the last sample. I receive the following error message for that sample:
[2013-05-28 22:02:25] Beginning TopHat run (v2.0.8b)
-----------------------------------------------
[2013-05-28 22:02:25] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-05-28 22:02:25] Checking for Samtools
Samtools version: 0.1.9.0
[2013-05-28 22:02:25] Checking for Bowtie index files
[2013-05-28 22:02:25] Checking for reference FASTA file
[2013-05-28 22:02:25] Generating SAM header for /data/genomes/hg19/genome/Bowtie2index/hg19
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[2013-05-28 22:02:30] Preparing reads
[FAILED]
Error running 'prep_reads'
---------------------------
My prep_reads.log is empty.
I would be very happy if anyone could tell me how to solve the problem!
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