Hi I was running Tophat on 1 FASTQ file and after a while of running, I got this error message in Bowtie that terminated my run. Could anybody give me some insight on this? HDD space should be plenty. Thanks!
Code:
[2013-01-16 14:59:34] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2013-01-16 14:59:34] Checking for Bowtie Bowtie 2 not found, checking for older version.. Bowtie version: 0.12.9.0 [2013-01-16 14:59:34] Checking for Samtools Samtools version: 0.1.18.0 [2013-01-16 14:59:34] Checking for Bowtie index files [2013-01-16 14:59:34] Checking for reference FASTA file Warning: Could not find FASTA file /home/mmy/bowtie-indexes/home/mmy/bowtie-indexes/mm9.fa [2013-01-16 14:59:34] Reconstituting reference FASTA file from Bowtie index Executing: /home/mmy/bin/bowtie-inspect /home/mmy/bowtie-indexes/mm9 > ./tophat_out/tmp/mm9.fa [2013-01-16 15:01:31] Generating SAM header for /home/mmy/bowtie-indexes/mm9 format: fastq quality scale: phred33 (default) [2013-01-16 15:01:54] Preparing reads left reads: min. length=50, max. length=50, 42714078 kept reads (131849 discarded) [2013-01-16 15:10:06] Mapping left_kept_reads to genome mm9 with Bowtie [2013-01-16 17:15:01] Mapping left_kept_reads_seg1 to genome mm9 with Bowtie (1/2) [2013-01-16 18:20:20] Mapping left_kept_reads_seg2 to genome mm9 with Bowtie (2/2) [2013-01-16 19:22:55] Searching for junctions via segment mapping [2013-01-16 20:19:25] Retrieving sequences for splices [2013-01-16 20:21:32] Indexing splices [2013-01-16 20:38:51] Mapping left_kept_reads_seg1 to genome segment_juncs with Bowtie (1/2) [COLOR="Red"]gzip: stdout: Broken pipe [FAILED] Error running bowtie: Error while flushing and closing output[/COLOR] Command: /home/mmy/bin/bowtie -q -v 2 -k 40 -m 40 -S -p 1 --sam-nohead --max /dev/null ./tophat_out/tmp/segment_juncs -