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