Hi everyone,
I have a *.qual file and I ran Tophat on the public galaxy server but I got
the following error. I am wondering if anyone has a solution for this.
Thank you
Input: QUAL Groomer file
Database: hg19 Full
Error:
Error in tophat:
[Tue Jan 17 10:55:08 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Tue Jan 17 10:55:08 2012] Preparing output location ./tophat_out/
[Tue Jan 17 10:55:08 2012] Checking for Bowtie index files
[Tue Jan 17 10:55:08 2012] Checking for reference FASTA file
[Tue Jan 17 10:55:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jan 17 10:55:08 2012] Checking for Samtools
Samtools Version: 0.1.12
[Tue Jan 17 10:55:08 2012] Generating SAM header for
/galaxy/data/hg19/hg19full/bowtie_index/hg19full
format: fastq
quality scale: phred33 (default)
[Tue Jan 17 10:55:34 2012] Preparing reads
left reads: min. length=50, count=5247
[Tue Jan 17 10:55:34 2012] Mapping left_kept_reads against hg19full with Bowtie
[Tue Jan 17 10:55:36 2012] Processing bowtie hits
[Tue Jan 17 10:57:03 2012] Mapping left_kept_reads_seg1 against
hg19full with Bowtie (1/21)
[Tue Jan 17 10:57:04 2012] Mapping left_kept_reads_seg2 against
hg19full with Bowtie (2/21)
[Tue Jan 17 10:57:05 2012] Mapping left_kept_reads_seg3 against
hg19full with Bowtie (3/21)
[Tue Jan 17 10:57:07 2012] Mapping left_kept_reads_seg4 against
hg19full with Bowtie (4/21)
[Tue Jan 17 10:57:08 2012] Mapping left_kept_reads_seg5 against
hg19full with Bowtie (5/21)
[Tue Jan 17 10:57:10 2012] Mapping left_kept_reads_seg6 against
hg19full with Bowtie (6/21)
[Tue Jan 17 10:57:11 2012] Mapping left_kept_reads_seg7 against
hg19full with Bowtie (7/21)
[Tue Jan 17 10:57:12 2012] Mapping left_kept_reads_seg8 against
hg19full with Bowtie (8/21)
[Tue Jan 17 10:57:13 2012] Mapping left_kept_reads_seg9 against
hg19full with Bowtie (9/21)
[Tue Jan 17 10:57:15 2012] Mapping left_kept_reads_seg10 against
hg19full with Bowtie (10/21)
[Tue Jan 17 10:57:16 2012] Mapping left_kept_reads_seg11 against
hg19full with Bowtie (11/21)
[Tue Jan 17 10:57:17 2012] Mapping left_kept_reads_seg12 against
hg19full with Bowtie (12/21)
[Tue Jan 17 10:57:18 2012] Mapping left_kept_reads_seg13 against
hg19full with Bowtie (13/21)
[Tue Jan 17 10:57:19 2012] Mapping left_kept_reads_seg14 against
hg19full with Bowtie (14/21)
[Tue Jan 17 10:57:20 2012] Mapping left_kept_reads_seg15 against
hg19full with Bowtie (15/21)
[Tue Jan 17 10:57:21 2012] Mapping left_kept_reads_seg16 against
hg19full with Bowtie (16/21)
[Tue Jan 17 10:57:22 2012] Mapping left_kept_reads_seg17 against
hg19full with Bowtie (17/21)
[Tue Jan 17 10:57:23 2012] Mapping left_kept_reads_seg18 against
hg19full with Bowtie (18/21)
[Tue Jan 17 10:57:24 2012] Mapping left_kept_reads_seg19 against
hg19full with Bowtie (19/21)
[Tue Jan 17 10:57:25 2012] Mapping left_kept_reads_seg20 against
hg19full with Bowtie (20/21)
[Tue Jan 17 10:57:26 2012] Mapping left_kept_reads_seg21 against
hg19full with Bowtie (21/21)
[Tue Jan 17 10:57:27 2012] Searching for junctions via segment mapping
[Tue Jan 17 10:58:42 2012] Retrieving sequences for splices
[Tue Jan 17 11:02:24 2012] Indexing splices
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg1 against
segment_juncs with Bowtie (1/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg2 against
segment_juncs with Bowtie (2/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg3 against
segment_juncs with Bowtie (3/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg4 against
segment_juncs with Bowtie (4/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg5 against
segment_juncs with Bowtie (5/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg6 against
segment_juncs with Bowtie (6/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg7 against
segment_juncs with Bowtie (7/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg8 against
segment_juncs with Bowtie (8/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg9 against
segment_juncs with Bowtie (9/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg10 against
segment_juncs with Bowtie (10/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg11 against
segment_juncs with Bowtie (11/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg12 against
segment_juncs with Bowtie (12/21)
[Tue Jan 17 11:02:25 2012] Mapping left_kept_reads_seg13 against
segment_juncs with Bowtie (13/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg14 against
segment_juncs with Bowtie (14/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg15 against
segment_juncs with Bowtie (15/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg16 against
segment_juncs with Bowtie (16/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg17 against
segment_juncs with Bowtie (17/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg18 against
segment_juncs with Bowtie (18/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg19 against
segment_juncs with Bowtie (19/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg20 against
segment_juncs with Bowtie (20/21)
[Tue Jan 17 11:02:26 2012] Mapping left_kept_reads_seg21 against
segment_juncs with Bowtie (21/21)
[Tue Jan 17 11:02:26 2012] Joining segment hits
[FAILED]
Error executing:
/galaxy/mounts/software/linux2.6-x86_64/pkg/tophat-1.4.0/bin/bam_merge
./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam
./tophat_out/tmp/left_kept_reads.candidates.bam
./tophat_out/tmp/left_kept_reads.unspl.bam
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