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Old 06-24-2011, 01:23 PM   #1
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Location: Maryland

Join Date: Jun 2011
Posts: 4
Default Problems with mapping SOLID color space sequences to hg19 using TopHat


I got a problem when mapping SOLID short sequences to hg19 using tophat. The human UCSC hg19 color space index was downloaded from bowtie website( The variant, $bowtieInputFile, in the following command, is the name of the fastq file. I have used the same command line, except omiting argument -C (which is specially for color space), to successfully map base space reads to hg19. But the problem, "segment-based junction search failed with err =1", always show up when doing color space mapping at the step "Searching for junctions via segment mapping".

Do you guys have any idea how I can avoid this problem?

Thanks in advance!


> tophat --solexa-quals -p 12 -C --output-dir tophat.output ~/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c $bowtieInputFile | tee -a fastq2bigwig.log

[Fri Jun 24 16:11:08 2011] Beginning TopHat run (v1.3.0)
[Fri Jun 24 16:11:08 2011] Preparing output location tophat.output/
[Fri Jun 24 16:11:08 2011] Checking for Bowtie index files
[Fri Jun 24 16:11:08 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c.fa
[Fri Jun 24 16:11:08 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /home/david/bin/bowtie-inspect /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c > tophat.output/tmp/hg19_c.fa
[Fri Jun 24 16:13:12 2011] Checking for Bowtie
Bowtie version:
[Fri Jun 24 16:13:12 2011] Checking for Samtools
Samtools Version: 0.1.16
[Fri Jun 24 16:13:12 2011] Generating SAM header for /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c
[Fri Jun 24 16:13:13 2011] Preparing reads
format: fastq
quality scale: solexa33 (reads generated with GA pipeline version < 1.3)
Left reads: min. length=51, count=737097
[Fri Jun 24 16:13:26 2011] Mapping left_kept_reads against hg19_c with Bowtie
[Fri Jun 24 16:13:46 2011] Processing bowtie hits
[Fri Jun 24 16:15:16 2011] Mapping left_kept_reads_seg1 against hg19_c with Bowtie (1/2)
[Fri Jun 24 16:16:03 2011] Mapping left_kept_reads_seg2 against hg19_c with Bowtie (2/2)
[Fri Jun 24 16:16:50 2011] Searching for junctions via segment mapping
Error: segment-based junction search failed with err =1
davidehs is offline   Reply With Quote
Old 06-24-2011, 02:21 PM   #2
Location: Denver, CO

Join Date: Mar 2011
Posts: 37

had the same error. you may want to give the new version (Tophat 1.3.1) a try since there were some SOLiD specific fixes in it. if that doesn't work, i've had some luck rolling back to 1.2.0, and, more routinely, use abi's aligner.
jbrwn is offline   Reply With Quote

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