Hi All,
I'm running into problems with Tophat; keep getting the following error:-
Error: segment-based junction search failed with err =-6.
This is HiSeq 100bp PE data.
Any ideas?
Cheers
Steve
##
[Mon Jul 18 16:27:43 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Mon Jul 18 16:27:43 2011] Preparing output location ./AST1.chr.9.tiling.bicep.smooth.muscle.july.2011/
[Mon Jul 18 16:27:43 2011] Checking for Bowtie index files
[Mon Jul 18 16:27:43 2011] Checking for reference FASTA file
[Mon Jul 18 16:27:43 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Jul 18 16:27:43 2011] Checking for Samtools
Samtools Version: 0.1.15
[Mon Jul 18 16:27:43 2011] Generating SAM header for /scratch/data/reference_genomes/human/human_g1k_v37
[Mon Jul 18 16:28:02 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[Mon Jul 18 16:28:02 2011] Reading known junctions from GTF file
Left reads: min. length=100, count=151802002
Right reads: min. length=100, count=151646210
[Mon Jul 18 19:11:17 2011] Mapping left_kept_reads against human_g1k_v37 with Bowtie
[Mon Jul 18 21:11:50 2011] Processing bowtie hits
[Mon Jul 18 23:05:38 2011] Mapping left_kept_reads_seg1 against human_g1k_v37 with Bowtie (1/4)
[Tue Jul 19 02:45:12 2011] Mapping left_kept_reads_seg2 against human_g1k_v37 with Bowtie (2/4)
[Tue Jul 19 06:18:55 2011] Mapping left_kept_reads_seg3 against human_g1k_v37 with Bowtie (3/4)
[Tue Jul 19 09:49:52 2011] Mapping left_kept_reads_seg4 against human_g1k_v37 with Bowtie (4/4)
[Tue Jul 19 13:22:18 2011] Mapping right_kept_reads against human_g1k_v37 with Bowtie
[Tue Jul 19 15:00:03 2011] Processing bowtie hits
[Tue Jul 19 16:53:27 2011] Mapping right_kept_reads_seg1 against human_g1k_v37 with Bowtie (1/4)
[Tue Jul 19 21:01:46 2011] Mapping right_kept_reads_seg2 against human_g1k_v37 with Bowtie (2/4)
[Wed Jul 20 00:52:22 2011] Mapping right_kept_reads_seg3 against human_g1k_v37 with Bowtie (3/4)
[Wed Jul 20 04:31:58 2011] Mapping right_kept_reads_seg4 against human_g1k_v37 with Bowtie (4/4)
[Wed Jul 20 08:07:07 2011] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =-6
I'm running into problems with Tophat; keep getting the following error:-
Error: segment-based junction search failed with err =-6.
This is HiSeq 100bp PE data.
Any ideas?
Cheers
Steve
##
[Mon Jul 18 16:27:43 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------
[Mon Jul 18 16:27:43 2011] Preparing output location ./AST1.chr.9.tiling.bicep.smooth.muscle.july.2011/
[Mon Jul 18 16:27:43 2011] Checking for Bowtie index files
[Mon Jul 18 16:27:43 2011] Checking for reference FASTA file
[Mon Jul 18 16:27:43 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Jul 18 16:27:43 2011] Checking for Samtools
Samtools Version: 0.1.15
[Mon Jul 18 16:27:43 2011] Generating SAM header for /scratch/data/reference_genomes/human/human_g1k_v37
[Mon Jul 18 16:28:02 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[Mon Jul 18 16:28:02 2011] Reading known junctions from GTF file
Left reads: min. length=100, count=151802002
Right reads: min. length=100, count=151646210
[Mon Jul 18 19:11:17 2011] Mapping left_kept_reads against human_g1k_v37 with Bowtie
[Mon Jul 18 21:11:50 2011] Processing bowtie hits
[Mon Jul 18 23:05:38 2011] Mapping left_kept_reads_seg1 against human_g1k_v37 with Bowtie (1/4)
[Tue Jul 19 02:45:12 2011] Mapping left_kept_reads_seg2 against human_g1k_v37 with Bowtie (2/4)
[Tue Jul 19 06:18:55 2011] Mapping left_kept_reads_seg3 against human_g1k_v37 with Bowtie (3/4)
[Tue Jul 19 09:49:52 2011] Mapping left_kept_reads_seg4 against human_g1k_v37 with Bowtie (4/4)
[Tue Jul 19 13:22:18 2011] Mapping right_kept_reads against human_g1k_v37 with Bowtie
[Tue Jul 19 15:00:03 2011] Processing bowtie hits
[Tue Jul 19 16:53:27 2011] Mapping right_kept_reads_seg1 against human_g1k_v37 with Bowtie (1/4)
[Tue Jul 19 21:01:46 2011] Mapping right_kept_reads_seg2 against human_g1k_v37 with Bowtie (2/4)
[Wed Jul 20 00:52:22 2011] Mapping right_kept_reads_seg3 against human_g1k_v37 with Bowtie (3/4)
[Wed Jul 20 04:31:58 2011] Mapping right_kept_reads_seg4 against human_g1k_v37 with Bowtie (4/4)
[Wed Jul 20 08:07:07 2011] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =-6
Comment