Hi all,
I just tested Tophat2.03 released on May 26th using a small data set (paired-end data, 5000 reads, read len = 50). Unfortunately, I got the error message below. I am not sure if I made something wrong or it is a bug...
[ao@xxxx tmp]$ tophat2 -r 150 -p 20 -g 1 -o ./ ../../bowtie2_index_hg19/hg19 tmp1.fq tmp2.fq
[2012-05-28 23:28:16] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-05-28 23:28:53] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-05-28 23:28:54] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-28 23:28:54] Checking for Bowtie index files
[2012-05-28 23:28:54] Checking for reference FASTA file
[2012-05-28 23:28:54] Generating SAM header for ../../bowtie2_index_hg19/hg19
format: fastq
quality scale: phred33 (default)
[2012-05-28 23:30:36] Preparing reads
left reads: min. length=50, max. length=50, 2498 kept reads (2 discarded)
right reads: min. length=50, max. length=50, 2494 kept reads (6 discarded)
[2012-05-28 23:35:13] Mapping left_kept_reads to genome hg19 with Bowtie2
[FAILED]
Error running:
/../tools/tophat-2.0.3/bam2fastx --all --fastq .//tmp/left_kept_reads.bam|/RIS/home/hzhao1/tools/bowtie2-2.0.0-beta6/bowtie2-align -q -k 1 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min L,-0.6,-0.6 -p 20 --sam-no-hd -x ../../bowtie2_index_hg19/hg19 -|/../tools/tophat-2.0.3/fix_map_ordering --bowtie2-min-score 10 --sam-header .//tmp/hg19_genome.bwt.samheader.sam - .//tmp/left_kept_reads.mapped.bam .//tmp/left_kept_reads_unmapped.bam --index-outfile .//tmp/left_kept_reads.mapped.bam.index
I just tested Tophat2.03 released on May 26th using a small data set (paired-end data, 5000 reads, read len = 50). Unfortunately, I got the error message below. I am not sure if I made something wrong or it is a bug...
[ao@xxxx tmp]$ tophat2 -r 150 -p 20 -g 1 -o ./ ../../bowtie2_index_hg19/hg19 tmp1.fq tmp2.fq
[2012-05-28 23:28:16] Beginning TopHat run (v2.0.3)
-----------------------------------------------
[2012-05-28 23:28:53] Checking for Bowtie
Bowtie version: 2.0.0.6
[2012-05-28 23:28:54] Checking for Samtools
Samtools version: 0.1.18.0
[2012-05-28 23:28:54] Checking for Bowtie index files
[2012-05-28 23:28:54] Checking for reference FASTA file
[2012-05-28 23:28:54] Generating SAM header for ../../bowtie2_index_hg19/hg19
format: fastq
quality scale: phred33 (default)
[2012-05-28 23:30:36] Preparing reads
left reads: min. length=50, max. length=50, 2498 kept reads (2 discarded)
right reads: min. length=50, max. length=50, 2494 kept reads (6 discarded)
[2012-05-28 23:35:13] Mapping left_kept_reads to genome hg19 with Bowtie2
[FAILED]
Error running:
/../tools/tophat-2.0.3/bam2fastx --all --fastq .//tmp/left_kept_reads.bam|/RIS/home/hzhao1/tools/bowtie2-2.0.0-beta6/bowtie2-align -q -k 1 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min L,-0.6,-0.6 -p 20 --sam-no-hd -x ../../bowtie2_index_hg19/hg19 -|/../tools/tophat-2.0.3/fix_map_ordering --bowtie2-min-score 10 --sam-header .//tmp/hg19_genome.bwt.samheader.sam - .//tmp/left_kept_reads.mapped.bam .//tmp/left_kept_reads_unmapped.bam --index-outfile .//tmp/left_kept_reads.mapped.bam.index
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