Re: [galaxy-dev] [galaxy-user] Tophat error
Hi Jen, Many thanks for this, much appreciated. Will give it a try - fingers crossed! David. Sent from my phone, so please excuse my mistakes. -Original Message- From: Jennifer Jackson Sent: 20/03/2012 18:32 To: David Matthews; Galaxy Dev Cc: galaxy-user; Jeremy Goecks Subject: Re: [galaxy-dev] [galaxy-user] Tophat error Hi David, I don't know if you are still having this problem or not, but I did a web search and found this thread on seqanswers from 2/16 that seems like a good match to the problem you were having: http://seqanswers.com/forums/showthread.php?p=65085 These scientists resolved the problem by removing the --closure-search option from the command string. On the Galaxy tool form, this is the option Use Closure Search:. which is No by default. Perhaps you set this to be Yes? I would try switching it to No to see if that solves the problem. If not, then contacting the tool authors would probably be the best next step, either at seqanswers or directly at tophat.cuffli...@gmail.com. The original guess about genome indexes was way off base, this is a python error statement. I don't believe this to be related to the Galaxy wrapper but will cc Jeremy for a second opinion. Hopefully the first option will resolve the issue! Thanks, Jen Galaxy team On 3/14/12 11:10 AM, Jennifer Jackson wrote: Hi David, You question has posted to the list now and we will be getting back to you. It didn't post immediately due to some mail mailman server issues here. This looks like a problem that came up on a local instance. Because of that, I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At first glance, this appears to be a problem with the NGS genome indexes used for the target genome. These are the instructions you followed? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used for TopHat) We will be looking at this more later today, but I wanted to get back to you, so you that you know that this doesn't need to be posted again. Thanks! Jen Galaxy team On 3/14/12 6:48 AM, David Matthews wrote: Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list
Re: [galaxy-dev] [galaxy-user] Tophat error
Hi David, I don't know if you are still having this problem or not, but I did a web search and found this thread on seqanswers from 2/16 that seems like a good match to the problem you were having: http://seqanswers.com/forums/showthread.php?p=65085 These scientists resolved the problem by removing the --closure-search option from the command string. On the Galaxy tool form, this is the option Use Closure Search:. which is No by default. Perhaps you set this to be Yes? I would try switching it to No to see if that solves the problem. If not, then contacting the tool authors would probably be the best next step, either at seqanswers or directly at tophat.cuffli...@gmail.com. The original guess about genome indexes was way off base, this is a python error statement. I don't believe this to be related to the Galaxy wrapper but will cc Jeremy for a second opinion. Hopefully the first option will resolve the issue! Thanks, Jen Galaxy team On 3/14/12 11:10 AM, Jennifer Jackson wrote: Hi David, You question has posted to the list now and we will be getting back to you. It didn't post immediately due to some mail mailman server issues here. This looks like a problem that came up on a local instance. Because of that, I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At first glance, this appears to be a problem with the NGS genome indexes used for the target genome. These are the instructions you followed? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used for TopHat) We will be looking at this more later today, but I wanted to get back to you, so you that you know that this doesn't need to be posted again. Thanks! Jen Galaxy team On 3/14/12 6:48 AM, David Matthews wrote: Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] [galaxy-user] Tophat error
Hi, Thanks for the reply, sorry about the multiple posts - it kept getting bounced so I resubmitted the question. We seem to be having real problems with our local install so I'll add it to the list...! Cheers David On 14 Mar 2012, at 18:10, Jennifer Jackson wrote: Hi David, You question has posted to the list now and we will be getting back to you. It didn't post immediately due to some mail mailman server issues here. This looks like a problem that came up on a local instance. Because of that, I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At first glance, this appears to be a problem with the NGS genome indexes used for the target genome. These are the instructions you followed? http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used for TopHat) We will be looking at this more later today, but I wanted to get back to you, so you that you know that this doesn't need to be posted again. Thanks! Jen Galaxy team On 3/14/12 6:48 AM, David Matthews wrote: Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule sys.exit(main()) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main user_supplied_deletions) File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
