I have run into the same problem that are few people have encountered before when I am using TopHat to align 7 lanes of Illumina data to hg19. Since I am relatively new to tophat, can somebody give me a hint? Thanks!
here are the screen output and segment_juncs.log:
segment_juncs.log
here are the screen output and segment_juncs.log:
Code:
[Fri Aug 20 14:58:12 2010] Beginning TopHat run (v1.0.13) ----------------------------------------------- [Fri Aug 20 14:58:12 2010] Preparing output location /home/haiti/tmpdata/all_brn/tophat/ [Fri Aug 20 14:58:12 2010] Checking for Bowtie index files [Fri Aug 20 14:58:12 2010] Checking for reference FASTA file [Fri Aug 20 14:58:12 2010] Checking for Bowtie Bowtie version: 0.12.5.0 [Fri Aug 20 14:58:12 2010] Checking reads seed length: 35bp format: fastq quality scale: phred33 (default) [Fri Aug 20 15:31:58 2010] Reading known junctions from GFF file Warning: TopHat did not find any junctions in GFF file [Fri Aug 20 15:53:49 2010] Mapping reads against hg19 with Bowtie [Sat Aug 21 00:52:55 2010] Joining segment hits [Sat Aug 21 01:22:40 2010] Searching for junctions via segment mapping [FAILED] Error: segment-based junction search failed with err = -9
Code:
segment_juncs v1.0.13 --------------------------- Loading reference sequences... Loading chr1...done Loading chr2...done Loading chr3...done Loading chr4...done Loading chr5...done Loading chr6...done Loading chr7...done Loading chr8...done Loading chr9...done Loading chr10...done Loading chr11...done Loading chr12...done Loading chr13...done Loading chr14...done Loading chr15...done Loading chr16...done Loading chr17...done Loading chr18...done Loading chr19...done Loading chr20...done Loading chr21...done Loading chr22...done Loading chrX...done Loading chrY...done Loading chrM...done Found 0 potential split-segment junctions Indexing extensions in /home/haiti/tmpdata/all_brn/tophat/tmp//left_kept_reads_missing.fq Total extensions: 637479408 Looking for junctions by island end pairings Adding hits from segment file 0 to coverage map Map covers 325972654 bases Map covers 320327918 bases in sufficiently long segments Map contains 5580241 good islands 276495363 are left looking bases 276492492 are right looking bases Collecting potential splice sites in islands
Comment