TopHat error bam2fastx

[npochet]

Hi,

Has anyone seen this error below before and knows how to solve it? I'm using TopHat2 version 2.0.9 with Bowtie2 2.1.0. I get this same error message for all my 20 samples. Any help is greatly appreciated.

Thanks much,
Nathalie

tophat-2.0.9.Linux_x86_64/tophat2 --fusion-search --num-threads 6 --library-type fr-unstranded --fusion-min-dist 0 -G gencode.v12.annotation.patched_contigs.gtf Homo_sapiens_assembly19 sample44.r1.fastq sample44.r2.fastq

[2013-06-28 17:02:45] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-06-28 17:02:45] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-06-28 17:02:45] Checking for Samtools
Samtools version: 0.1.9.0
[2013-06-28 17:02:45] Checking for Bowtie index files (genome)..
[2013-06-28 17:02:45] Checking for reference FASTA file
[2013-06-28 17:02:45] Generating SAM header for Homo_sapiens_assembly19
format: fastq
quality scale: phred33 (default)
[2013-06-28 17:02:47] Reading known junctions from GTF file
[2013-06-28 17:03:11] Preparing reads
left reads: min. length=50, max. length=50, 10940289 kept reads (5032 discarded)
right reads: min. length=50, max. length=50, 10486807 kept reads (458514 discarded)
[2013-06-28 17:07:21] Building transcriptome data files..
[2013-06-28 17:09:37] Building Bowtie index from gencode.v12.annotation.patched_contigs.fa
[2013-06-28 19:30:31] Mapping left_kept_reads to transcriptome gencode.v12.annotation.patched_contigs with Bowtie2
[FAILED]
Error running:
tophat-2.0.9.Linux_x86_64/bam2fastx --all --fastq ./tophat_out/tmp/left_kept_reads.bam|bowtie2-2.1.0/bowtie2-align -q -k 60 -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 C,-14,0 -p 6 --sam-no-hd -x ./tophat_out/tmp/gencode.v12.annotation.patched_contigs -|tophat-2.0.9.Linux_x86_64/fix_map_ordering --bowtie2-min-score 15 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --sam-header ./tophat_out/tmp/gencode.v12.annotation.patched_contigs.bwt.samheader.sam - - ./tophat_out/tmp/left_kept_reads.m2g_um.bam | tophat-2.0.9.Linux_x86_64/map2gtf --sam-header ./tophat_out/tmp/Homo_sapiens_assembly19_genome.bwt.samheader.sam ./tophat_out/tmp/gencode.v12.annotation.patched_contigs.fa.tlst - ./tophat_out/tmp/left_kept_reads.m2g.bam > ./tophat_out/logs/m2g_left_kept_reads.out