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Trackster error: indexing
by Nancy Au Yeung 14 Jul '12

14 Jul '12

Hi, I saw another post regarding trackster error and it seems like this is different. I have tried copying the dataset from the History option, but this same error occurs. See error script below. Thanks! Trackster Error *** glibc detected *** python: double free or corruption (top): 0x0000000001c09370 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x75ab6)[0x7f93fe421ab6] /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f93fe4267ec] /lib/x86_64-linux-gnu/libc.so.6(fclose+0x14d)[0x7f93fe412a0d] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(bam_index_load_literal+0x37)[0x7f93fdac2ad7] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x6e7f8)[0x7f93fdaae7f8] python(PyObject_Call+0x36)[0x4824c6] python(PyEval_CallObjectWithKeywords+0x36)[0x486086] /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so(+0x52a04)[0x7f93fda92a04] python[0x482068] python(PyObject_Call+0x36)[0x4824c6] python(PyEval_EvalFrameEx+0x91a)[0x4c5e8a] python(PyEval_EvalCodeEx+0x136)[0x4ccee6] python(PyEval_EvalFrameEx+0x838)[0x4c5da8] python(PyEval_EvalCodeEx+0x136)[0x4ccee6] python(PyRun_FileExFlags+0xe1)[0x577901] python(PyRun_SimpleFileExFlags+0x177)[0x577b37] python(Py_Main+0x6f7)[0x550497] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xfd)[0x7f93fe3caead] python[0x41dea1] ======= Memory map: ======== 00400000-00672000 r-xp 00000000 fe:00 893421 /usr/bin/python2.7 00871000-00872000 r--p 00271000 fe:00 893421 /usr/bin/python2.7 00872000-008db000 rw-p 00272000 fe:00 893421 /usr/bin/python2.7 008db000-008ed000 rw-p 00000000 00:00 0 0166d000-01c29000 rw-p 00000000 00:00 0 [heap] 7f93f8000000-7f93f8021000 rw-p 00000000 00:00 0 7f93f8021000-7f93fc000000 ---p 00000000 00:00 0 7f93fd6de000-7f93fd70e000 r-xp 00000000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd70e000-7f93fd80d000 ---p 00030000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd80d000-7f93fd812000 rw-p 0002f000 00:18 458639 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/ctabix.so 7f93fd812000-7f93fd814000 rw-p 00000000 00:00 0 7f93fd814000-7f93fd83b000 r-xp 00000000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fd83b000-7f93fda3a000 ---p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3a000-7f93fda3b000 r--p 00026000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3b000-7f93fda3f000 rw-p 00027000 fe:00 949810 /usr/lib/python2.7/lib-dynload/_ctypes.so 7f93fda3f000-7f93fda40000 rw-p 00000000 00:00 0 7f93fda40000-7f93fdb10000 r-xp 00000000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdb10000-7f93fdc10000 ---p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdc10000-7f93fdc20000 rw-p 000d0000 00:18 458638 /galaxy/home/g2main/galaxy_main/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/csamtools.so 7f93fdc20000-7f93fdc25000 rw-p 00000000 00:00 0 7f93fdc25000-7f93fdc44000 r-xp 00000000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fdc44000-7f93fde44000 ---p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde44000-7f93fde45000 r--p 0001f000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde45000-7f93fde4e000 rw-p 00020000 fe:00 949804 /usr/lib/python2.7/lib-dynload/_io.so 7f93fde4e000-7f93fdf0f000 rw-p 00000000 00:00 0 7f93fdf0f000-7f93fdf12000 r-xp 00000000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fdf12000-7f93fe111000 ---p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe111000-7f93fe112000 r--p 00002000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe112000-7f93fe114000 rw-p 00003000 fe:00 949801 /usr/lib/python2.7/lib-dynload/_heapq.so 7f93fe114000-7f93fe196000 rw-p 00000000 00:00 0 7f93fe196000-7f93fe1ab000 r-xp 00000000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe1ab000-7f93fe3ab000 ---p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe3ab000-7f93fe3ac000 rw-p 00015000 fe:00 122656 /lib/x86_64-linux-gnu/libgcc_s.so.1 7f93fe3ac000-7f93fe529000 r-xp 00000000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe529000-7f93fe729000 ---p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe729000-7f93fe72d000 r--p 0017d000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe72d000-7f93fe72e000 rw-p 00181000 fe:00 131366 /lib/x86_64-linux-gnu/libc-2.13.so 7f93fe72e000-7f93fe733000 rw-p 00000000 00:00 0 7f93fe733000-7f93fe7b4000 r-xp 00000000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe7b4000-7f93fe9b3000 ---p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b3000-7f93fe9b4000 r--p 00080000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b4000-7f93fe9b5000 rw-p 00081000 fe:00 131404 /lib/x86_64-linux-gnu/libm-2.13.so 7f93fe9b5000-7f93fe9cb000 r-xp 00000000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93fe9cb000-7f93febca000 ---p 00016000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93febca000-7f93febcb000 rw-p 00015000 fe:00 909634 /usr/lib/x86_64-linux-gnu/libz.so.1.2.6 7f93febcb000-7f93fed68000 r-xp 00000000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fed68000-7f93fef67000 ---p 0019d000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fef67000-7f93fef8d000 rw-p 0019c000 fe:00 909753 /usr/lib/x86_64-linux-gnu/libcrypto.so.1.0.0 7f93fef8d000-7f93fef91000 rw-p 00000000 00:00 0 7f93fef91000-7f93fefdc000 r-xp 00000000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93fefdc000-7f93ff1db000 ---p 0004b000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93ff1db000-7f93ff1e3000 rw-p 0004a000 fe:00 909754 /usr/lib/x86_64-linux-gnu/libssl.so.1.0.0 7f93ff1e3000-7f93ff1e5000 r-xp 00000000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff1e5000-7f93ff3e4000 ---p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e4000-7f93ff3e5000 r--p 00001000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e5000-7f93ff3e6000 rw-p 00002000 fe:00 131419 /lib/x86_64-linux-gnu/libutil-2.13.so 7f93ff3e6000-7f93ff3e8000 r-xp 00000000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff3e8000-7f93ff5e8000 ---p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5e8000-7f93ff5e9000 r--p 00002000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5e9000-7f93ff5ea000 rw-p 00003000 fe:00 131412 /lib/x86_64-linux-gnu/libdl-2.13.so 7f93ff5ea000-7f93ff601000 r-xp 00000000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff601000-7f93ff800000 ---p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff800000-7f93ff801000 r--p 00016000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff801000-7f93ff802000 rw-p 00017000 fe:00 131416 /lib/x86_64-linux-gnu/libpthread-2.13.so 7f93ff802000-7f93ff806000 rw-p 00000000 00:00 0 7f93ff806000-7f93ff825000 r-xp 00000000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ff859000-7f93ff95d000 rw-p 00000000 00:00 0 7f93ff98f000-7f93ffa17000 rw-p 00000000 00:00 0 7f93ffa21000-7f93ffa22000 rw-p 00000000 00:00 0 7f93ffa22000-7f93ffa23000 rwxp 00000000 00:00 0 7f93ffa23000-7f93ffa25000 rw-p 00000000 00:00 0 7f93ffa25000-7f93ffa26000 r--p 0001f000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ffa26000-7f93ffa27000 rw-p 00020000 fe:00 131420 /lib/x86_64-linux-gnu/ld-2.13.so 7f93ffa27000-7f93ffa28000 rw-p 00000000 00:00 0 7fff744fb000-7fff7451c000 rw-p 00000000 00:00 0 [stack] 7fff74589000-7fff7458a000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted

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Galaxy Help!!
by Robby Quinn 13 Jul '12

13 Jul '12

I am trying to use LEfSe but keep getting the same error. My data loads fine, but then I cannot get results from 'Plot LEfSe Results'. I then try to report the error, but it consistently tells me 'Mail is not configured for this Galaxy instance". So I don't think my error reports are working. Help Please!!! 0 bytes An error occurred running this job:*Traceback (most recent call last): File "/usr/local/galaxy-dist/tools/lefse/plot_res.py", line 151, in <module> else: plot_histo_hor(params['output_file'],params,data,len(data['cls']) == 2) File "/usr/local/galaxy-dist/tools/lefse/plot_res.py", li* -- Robert Quinn, Ph.D CFRI Postdoctoral Fellow NLS 301, 5500 Campanile Dr, San Diego State University San Diego, CA, 92182

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Gene BED to codon BED not working properly
by Antony Jose 12 Jul '12

12 Jul '12

Hi, When using the gene BED to codon BED tool, I noticed that it is not accurately reporting the codons that make up a gene. For example, some of the codon are missing (particularly ones that span exon-exon junctions. Also, when changing reading frame from one exon to the next, the codons are not read appropriately and the reading frame appears to be decided arbitrarily. Is this a serious known flaw with the tool or am I missing something? Also, is there a version of aaChanges tool that can be used with any genome (not just human genome?). Thank you. Antony

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Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data
by Lindsey Kelly 11 Jul '12

11 Jul '12

I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check the quality using the FASTQqc tool I don't know how to handle this many files. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Thanks in advance for advice Lindsey

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metagenomics question
by Jennifer Jackson 11 Jul '12

11 Jul '12

Hello, The publication and supplemental material for the metagenomics data and tools available in Galaxy described in: Windshield splatter analysis with the Galaxy metagenomic pipeline is available on the main public Galaxy instance at: Shared Data -> Shared Published Pages -> Windshield Splatter http://genome.cshlp.org/content/19/11/2144 http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter All methods and tools are explained in detail, including example datasets, histories, workflows, and scientific discussion of results. Hopefully this help. Going forward, please send new questions as a brand new thread (not as a reply to an older thread) directly to our mailing list at galaxy-user(a)bx.psu.edu. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Best, Jen Galaxy team On 7/7/12 1:33 AM, Swayamprakash Patel wrote:> Hello, > i had run galaxy server for metagenomics study... but, i would like > to know that which database is used for the comparison... because in my > sample it had gives me highest no. of eukaryotic community. but actually > in my data there would be a bacterial community is present in more > numbers. that's why i have a question like this. -- Jennifer Jackson http://galaxyproject.org

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fetch codons and amino acid
by bingyu19821270 11 Jul '12

11 Jul '12

Hi all, I am a new Galaxy user and I have searched the mail list, looking for the answers to my questions, but failed. I am trying to fetch the corresponding codon or amino acid alignments among 46 species using genomic intervals in human. I know if I have a list of human genomic intervals, I can get the nucleotide alignments of these intervals among 46 species. I have hundreds of genomic intervals in human. They are all located in CDS regions. I already fetched the alignment among the 46 species for each genomic interval. The thing is that I also want to know the corresponding codons or amino acids. Can somebody help me out? Thanks a million! -------------------------------------------------------------------------------- Patricia Hsu Kunming Institute of botany, CAS bingyu19821270

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Tophat
by Jennifer Jackson 11 Jul '12

11 Jul '12

Hello, Using the defaults and then testing the resulting SAM output seems to be what most folks are doing if they do not have access to the original library construction methods (e.g. size selection). Both SAM Tools and Picard are in Galaxy. This is a useful post where the options are discussed: http://www.biostars.org/post/show/16556/estimate-insert-size-in-paired-endm… Is the data Illumina? The data source may be able to tell you if the adapter sequence was actually sequenced and/or if it was removed already or not. If present or you just suspect it is present, they would also have access to the Illumina fasta adapter data. You could also test with FastQC (before or after alignment, maybe on just a sample), then perform a clip based on those results, and re-run. See the tools in 'NGS: QC and manipulation' to perform these tasks. Going forward, please send questions as a new thread directly to our mailing list at galaxy-user(a)bx.psu.edu. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Best, Jen Galaxy team On 7/10/12 5:36 AM, asma.bioinfo(a)gmail.com wrote: > Does anyone got correct answer, how to extract the correct distance between two pairs? > > One naive question, how can I find the adapter sequence length? > > Thanks! -- Jennifer Jackson http://galaxyproject.org

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Re: [galaxy-user] Getting the installed data to show up in the sample files at run time
by Carlos Borroto 10 Jul '12

10 Jul '12

On Fri, Jul 6, 2012 at 3:07 AM, Aarti Desai <aarti_desai(a)persistent.co.in> wrote: > These show up in the history with the appropriate size. But when I choose > the “Map with BWA for Illumina” option, the two fastq files do not show up > in the FASTQ file drop down. Hi Aarti, Most tools in galaxy that work with fastq file need specifically fastqsanger input file. Even if your file have the quality values in Sanger format, the auto detect format logic won't be able to determine this. If you know you fastq file are in fact in Sanger format, editing your file metadata and selecting fastqsanger for the format would do the trick. If you aren't sure, you should use Fastq Groomer tool to convert them to Sanger format. I would recommend to watch the several screencast describing mapping analysis in Galaxy. Hope it helps, Carlos

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"job is waiting to run" forever
by Yehoshua Enuka 10 Jul '12

10 Jul '12

Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as "Job is waiting to run" forever. Could you please let me know the possible reasons? Sincerely, Enuka

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Indexing files everytime - Performance Issue
by Praveen Raj Somarajan 09 Jul '12

09 Jul '12

All, It is noticed that Galaxy/GATK indexes reference fasta & dbSNP file everytime when it runs. Re-indexing takes time (~10min), hence it affects overall run time when it use for multiple times. However, this could be avoided by reusing the available index. Here is the snapshot of the log: INFO 11:43:57,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-21-g30b937d, Compiled 2012/02/01 19:01:14 INFO 11:43:57,365 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:43:57,365 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 11:43:57,366 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 11:43:57,367 HelpFormatter - --------------------------------------------------------------------------------- INFO 11:43:57,429 GenomeAnalysisEngine - Strictness is STRICT INFO 11:43:57,432 ReferenceDataSource - Index file /tmp/tmp-gatk-6jlUfH/gatk_input.fasta.fai does not exist. Trying to create it now. PROGRESS UPDATE: file is 15 percent complete PROGRESS UPDATE: file is 28 percent complete PROGRESS UPDATE: file is 91 percent complete INFO 11:45:32,231 ReferenceDataSource - Dict file /tmp/tmp-gatk-6jlUfH/gatk_input.dict does not exist. Trying to create it now. INFO 11:45:54,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 11:45:54,280 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 11:45:54,304 RMDTrackBuilder - Creating Tribble index in memory for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf INFO 11:48:05,910 RMDTrackBuilder - Writing Tribble index to disk for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf.idx Do we have any option/alternate in Galaxy to avoid this re-indexing at /tmp, as I have already built the index for reference and dbSNP. Look forward to any suggestions. Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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