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
Hi Minh, Would you please submit the error as a bug report? Click on the green bug icon in the red error dataset and include any comments you feel are relevant. Be sure to leave the error dataset and any inputs in your history until we are able to provide feedback. If you want to try to troubleshoot first, please see this wiki for some tips: http://wiki.g2.bx.psu.edu/Support#Error_from_tools Best, Jen Galaxy team On 1/27/12 11:36 AM, Minh Bui wrote:
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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participants (2)
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Jennifer Jackson -
Minh Bui