Don't know where to post, so I just post here.
Originally posted by oliviera
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tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq [Mon Nov 15 12:52:59 2010] Beginning TopHat run (v1.1.0) ----------------------------------------------- [Mon Nov 15 12:52:59 2010] Preparing output location RNA-seq-14.11.10/tophat_out_0H// [Mon Nov 15 12:52:59 2010] Checking for Bowtie index files [Mon Nov 15 12:52:59 2010] Checking for reference FASTA file [Mon Nov 15 12:52:59 2010] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Nov 15 12:52:59 2010] Checking for Samtools Samtools version: 0.1.9.0 [Mon Nov 15 12:52:59 2010] Checking reads min read length: 36bp, max read length: 36bp format: fastq quality scale: phred64 (reads generated with GA pipeline version >= 1.3) [Mon Nov 15 12:55:49 2010] Reading known junctions from GTF file [FAILED] Error: could not execute prep_reads
tophat -o RNA-seq-14.11.10/tophat_out_0H -G maygtf.gtf --no-novel-juncs --solexa1.3-quals indexes/_May_2009-masked reads/RNA-seq/R43s_1_sequence_0H.fastq [Mon Nov 15 12:52:59 2010] Beginning TopHat run (v1.1.0) ----------------------------------------------- [Mon Nov 15 12:52:59 2010] Preparing output location RNA-seq-14.11.10/tophat_out_0H// [Mon Nov 15 12:52:59 2010] Checking for Bowtie index files [Mon Nov 15 12:52:59 2010] Checking for reference FASTA file [Mon Nov 15 12:52:59 2010] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Nov 15 12:52:59 2010] Checking for Samtools Samtools version: 0.1.9.0 [Mon Nov 15 12:52:59 2010] Checking reads min read length: 36bp, max read length: 36bp format: fastq quality scale: phred64 (reads generated with GA pipeline version >= 1.3) [Mon Nov 15 12:55:49 2010] Reading known junctions from GTF file [FAILED] Error: could not execute prep_reads
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