Hello sachit,
Sachit Adhikari <sachit.technerves@...> writes: > > > I am getting this error: > > Error in tophat: > > [2013-02-13 20:46:41] Beginning TopHat run (v2.0.7) > ----------------------------------------------- > [2013-02-13 20:46:41] Checking for Bowtie > Bowtie version: 2.0.6.0 > [2013-02-13 20:46:41] Checking for Samtools > Samtools version: 0.1.18.0 > [2013-02-13 20:46:41] Checking for Bowtie index files > [2013-02-13 20:46:41] Checking for reference FASTA file > Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa > [2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index > Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa > [2013-02-13 20:48:51] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > format: fastq > quality scale: phred33 (default) > [2013-02-13 20:49:23] Preparing reads > left reads: min. length=34, max. length=34, 2 kept reads (0 discarded) > Warning: you have only one segment per read. > If the read length is greater than or equal to 45bp, > we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments > [2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2 > [2013-02-13 20:49:56] Searching for junctions via segment mapping > Coverage-search algorithm is turned on, making this step very slow > Please try running TopHat again with the option (--no-coverage-search) > if this step takes too much time or memory. > Warning: junction database is empty! > [2013-02-13 20:51:18] Reporting output tracks > [FAILED] > Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam > Loading ...done > > What's wrong? > > > <div> > <p>I am getting this error:</p> > <div><br></div> > <div>Error in tophat: > > [2013-02-13 20:46:41] Beginning TopHat run (v2.0.7) > ----------------------------------------------- > [2013-02-13 20:46:41] Checking for Bowtie > Bowtie version: 2.0.6.0 > [2013-02-13 20:46:41] Checking for Samtools > Samtools version: 0.1.18.0 > [2013-02-13 20:46:41] Checking for Bowtie index files > [2013-02-13 20:46:41] Checking for reference FASTA file > Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa > [2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index > Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa > [2013-02-13 20:48:51] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > format: fastq > quality scale: phred33 (default) > [2013-02-13 20:49:23] Preparing reads > left reads: min. length=34, max. length=34, 2 kept reads (0 discarded) > Warning: you have only one segment per read. > If the read length is greater than or equal to 45bp, > we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments > [2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2 > [2013-02-13 20:49:56] Searching for junctions via segment mapping > Coverage-search algorithm is turned on, making this step very slow > Please try running TopHat again with the option (--no-coverage-search) > if this step takes too much time or memory. > Warning: junction database is empty! > [2013-02-13 20:51:18] Reporting output tracks > [FAILED] > Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam > Loading ...done > </div> > <div>What's wrong?</div> > </div> > even I am getting the same error. please let me know if you have solved it. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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