December 2013 - galaxy-user - lists.galaxyproject.org

Empty bowtie2 output
by IIHG Galaxy Administrator 10 Dec '13

10 Dec '13

In follow-up to http://user.list.galaxyproject.org/Empty-bowtie2-output-tp4656137.html, is there: - an ETA on when the issue with Bowtie2, in August 2013 distribution, generating empty output will be fixed (if not already fixed) ? - a suggested workaround (revert to an older version of that particular tool etc.) in the meantime ? Thank you. Unrelated: wasn't able to determine how to update that thread to request status, hence creating a new one.

2 1

Problem with executable file in FastQC
by Jorge Braun 09 Dec '13

09 Dec '13

Hi mates!! I have a problem with Galaxy... FastQC doesn't run because the file FastQC.py cann't find executable file FastQC.xml. Almost, that file is in the same directory called rgenetics, (seeing Linux terminal) . someone can help me? thanks and have a nice day :)

3 3

Trackster Error chrom/?.len , No such file or directory
by Jasper Jan Koehorst 05 Dec '13

05 Dec '13

I have my own genome fasta file containing 1 chromosome with a modified header so that it looks like: >chr1 ATGCATGC.... I did a FASTQ mapping on it via the galaxy interface and now I end up with a bam file: 9 Bowtie2 on data 6, data 8, and data 7: aligned reads 1.2 GB format bam database ? I use the visualize button to start the visualization of the dataset. I chose trackster, And view it in a new visualization. I use my fasta file as a reference genome: NameKeyNumber of chroms/contigsSTPmg315STPmg315_v11 But then I get the error: Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len , No such file or directory I looked into the /chrom/ folder and of course ? does not exist. I am currently running python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/ But this ofcourse downloads only known genomes and their chr. information. As I have my own genome I was curious how to continue with this. I manually created a file in the /chrom/so that it looks like this: *head STPmg315.len * chr1 1900521 but no luck so far. What else do I have to do to make it work? Thanks, Jasper

2 1

.Bam file upload and use problem
by Lu, Yuan (MU-Student) 04 Dec '13

04 Dec '13

Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I used galaxy server at PSU. I tried load local .bam file directly to galaxy, I also tried FTP, but both ways resulted into the same outcome. The .bam files I was using are pure .bam files with no index. Problems: 1.After I load them, the file was recognized as .txt file, and it is "empty" (But it did take long time to upload to FTP ~1GB), in the annotation window, it shows "The uploaded binary file contains inappropriate content" 2. I tried to convert the file to .bam format, it returns "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection." Anyone know how to solve this problem? Y.L.

2 1

Question on uploading and use .bam files
by Lu, Yuan (MU-Student) 04 Dec '13

04 Dec '13

Dear Sir or Madam, Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I used galaxy server at PSU. I tried load local .bam file directly to galaxy, I also tried FTP, but both ways resulted into the same outcome. The .bam files I was using are pure .bam files with no index. Problems: 1.After I load them, the file was recognized as .txt file, and it is "empty" (But it did take long time to upload to FTP ~1GB), in the annotation window, it shows "The uploaded binary file contains inappropriate content" 2. I tried to convert the file to .bam format, it returns "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection." Could you help me for this, I just uploaded a small file to the FTP, just in case you need it for a test. Username: ylc35(a)mail.missouri.edu Great thanks~ YL

2 1

Is there a problem with jobs on Galaxy today?
by Ruth Eberhardt 04 Dec '13

04 Dec '13

Hi Apologies if this is the wrong mailing list. Is there a problem with jobs running on Galaxy today? I have jobs (MACS and FASTQC) which have been waiting to run for a couple of hours. Manyt hanks Ruth

2 1

jobs not running
by Ruth Eberhardt 04 Dec '13

04 Dec '13

Hi Apologies if this is the wrong mailing list. Is there a problem with jobs running on Galaxy today? I have jobs (MACS and FASTQC) which have been waiting to run for over 4 hours, bit not yet started to run. Many thanks Ruth

2 1

Peak annotation with Galaxy
by Wooi Lim 03 Dec '13

03 Dec '13

Dear Galaxy, I am analysing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads with bowtie and did the peak calling with Macs. The next thing I wanted to do is to annotate the peaks with genomic regions i.e. promoter, intergenic, intron etc and gene names. I am not sure if these can be achieved through Galaxy and if so, how can this be done? Thank you. Catheryn

3 3

SNP finding
by Xiefan Fang 03 Dec '13

03 Dec '13

Dear galaxy users, We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. Thanks, Xiefan University of Florida

5 9

FW: [galaxy-bugs] Galaxy tool error report from bsib@leeds.ac.uk
by Irene Bassano 02 Dec '13

02 Dec '13

Hi Jen, thanks. I am a bit confused: on Galaxy the only human genome listed is hg_g1k_v37. So when I uploaded the new data from "Get data", under "Genome" I selected hg_g1k_v37 Now, all i want is to get cufflinks with gene names: which genome am I supposed to use? the only one I knew was hg19 from iGenomes...but seems i cannot use it. Do I have to select a genome when I upload raw fastq data? I havent stated doign anything so far, its just raw data Thanks a lot, Irene ________________________________________ From: Jennifer Jackson [jen(a)bx.psu.edu] Sent: Wednesday, November 27, 2013 10:08 PM To: Irene Bassano Cc: galaxy-bugs(a)bx.psu.edu Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib(a)leeds.ac.uk Hello, iGenomes covers the UCSC build, and this named "Human Feb. 2009 (GRCh37/hg19) (hg19)" in the full name in the UI. The "hg19" key is the important part - as the name may be abbreviated in some tools, but this key will be in all. The genome with the "hg_g1k_v37" key is slightly different and you will have another genome mismatch problem with the RNA-seq (and most other) tools if you combine this genome with data from UCSC (the source of hg19) or the wrong iGenomes file. "hg_g1k_v37" (source: 1000 genomes via GATK) and "hg19" (source: UCSC) are just about the same, but the identifiers are different. If you want to examine the differences, both are available on our rsync server and can be downloaded and compared. On the "Help -> Support" wiki are links for reference genomes. The iGenomes GTF file for hg19 is on the public Main server, if that is more convenient for you, or should you just want to be sure you have the right one. Look in Shared Data -> Data Libraries -> iGenomes. Best, Jen Galaxy team ps. please try to send new questions to one of our lists, thanks! On 11/27/13 12:51 PM, Irene Bassano wrote: > Hi Jen, > I uploaded some fastq files and selected as Genome from the drop down list ""Homo sapiens b37(hg_g1k_v37). > > Is this the same as the genome listed in UCSC "February 2009 (GRCh37/hg19)"? > > I am using iGenomes to get the gene names rather than annotation such as NM_00xxxx and I fused the UCSC website choosing the newest genome, February 2009 > > Thanks, > > best, > Irene > ________________________________________ > From: Jennifer Jackson [jen(a)bx.psu.edu] > Sent: Monday, November 18, 2013 7:26 PM > To: galaxy-bugs(a)bx.psu.edu; Irene Bassano > Subject: Re: [galaxy-bugs] Galaxy tool error report from bsib(a)leeds.ac.uk > > Hi again, > > The database mismatch is a problem here is well for the same reasons. My > guess is that you intended to run dataset #21 against hg19, and that the > run against hg18 was a tool form input mistake? > > Good luck with the next runs, > > Jen > Galaxy team > > On 11/18/13 5:21 AM, galaxy-bugs(a)bx.psu.edu wrote: >> GALAXY TOOL ERROR REPORT >> ------------------------ >> >> This error report was sent from the Galaxy instance hosted on the server >> "usegalaxy.org" >> ----------------------------------------------------------------------------- >> This is in reference to dataset id 7081835 from history id 1686699 >> ----------------------------------------------------------------------------- >> You should be able to view the history containing the related history item >> >> 37: Cufflinks on data 21 and data 34: assembled transcripts >> >> by logging in as a Galaxy admin user to the Galaxy instance referenced above >> and pointing your browser to the following link. >> >> usegalaxy.org/history/view?id=d88c1ef77619eb4f >> ----------------------------------------------------------------------------- >> The user 'bsib(a)leeds.ac.uk' provided the following information: >> >> Same as before but the reference genome is UCSC MAin on Human:refFlat >> ----------------------------------------------------------------------------- >> job id: 6096851 >> tool id: toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.6 >> job pid or drm id: 136948 >> ----------------------------------------------------------------------------- >> job command line: >> python /galaxy/main/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/b01956f26c36/cufflinks/cufflinks_wrapper.py --input=/galaxy-repl/main/files/007/074/dataset_7074022.dat --assembled-isoforms-output=/galaxy-repl/main/files/007/081/dataset_7081835.dat --num-threads="8" -I 300000 -F 0.1 -j 0.15 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -N -b --ref_file="None" --dbkey=hg18 --index_dir=/galaxy/main/server/tool-data -u >> ----------------------------------------------------------------------------- >> job stderr: >> Error running cufflinks. >> return code = 1 >> Command line: >> cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa /galaxy-repl/main/files/007/074/dataset_7074022.dat >> Error: cannot open reference GTF file /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat for reading >> >> >> ----------------------------------------------------------------------------- >> job stdout: >> cufflinks v2.1.1 >> cufflinks -q --no-update-check -I 300000 -F 0.100000 -j 0.150000 -p 8 -G /galaxy-repl/main/psufiles/004/831/dataset_4831015.dat -u -N -b /galaxy/data/hg18/sam_index/hg18.fa >> >> ----------------------------------------------------------------------------- >> job info: >> None >> ----------------------------------------------------------------------------- >> job traceback: >> None >> ----------------------------------------------------------------------------- >> (This is an automated message). > -- > Jennifer Hillman-Jackson > http://galaxyproject.org > -- Jennifer Hillman-Jackson http://galaxyproject.org

2 1

tophat issues
by miroslav.sotak 02 Dec '13

02 Dec '13

To whom it may concern I do have a problem with tophat. I can easily put fastq data to "history" and according to RNA-seq Analysis Exercise provided by Jeremy. We checked the type of Ascii ofset for the quality estimation. I tried even "quality data converter" set to 33 (we do have data of this ASCII offset from 2 different sources) but "tophat for Illumina" simply can not read the data before and even after quality format converter. We do not have any idea what is going on. I am logged in Galaxy with current email, can you check my data and is there any converter for quality offset? Sincerely Miro Sotak

2 1

Re: [galaxy-user] Problem loading BAM into IGV browser - invalid GZIP header error message
by Jim Johnson 02 Dec '13

02 Dec '13

Is galaxy returning an html page rather than the desired bam file? Are you using an nginx or apache proxy server to your galaxy server? I think that may be required, in order to view BAM files in IGV directly from Galaxy. JJ On 11/29/13, 11:00 AM, galaxy-user-request(a)lists.bx.psu.edu wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. > > Today's Topics: > > 1. Problem loading BAM into IGV browser - invalid GZIP header > error message (Vosberg, Sebastian) > 2. Re: Problem loading BAM into IGV browser - invalid GZIP > header error message (Jim Robinson) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 Nov 2013 11:04:48 +0100 > From: "Vosberg, Sebastian" <sebastian.vosberg(a)helmholtz-muenchen.de> > To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: [galaxy-user] Problem loading BAM into IGV browser - invalid > GZIP header error message > Message-ID: > <20854588711E4A489A3AD70C9BA5548A01AE291C4614(a)XCH11.scidom.de> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > > sometimes I encouter a problem trying to load BAM files directly from Galaxy into the IGV browser. First I am starting the IGV browser locally, then clicking on the appropriate BAM file and on "display with IGV _local_" in Galaxy. In most cases it works, but for some reasons not with specific files. The error message says > > "Error loading http://_URL-to-file_/galaxy_example.bam: An error occured while accessing http://_URL-to-file_/galaxy_example.bam > Invalid GZIP header" > > What does it mean? And why am I able to download the BAM file and load it from HDD into the IGV? > The problem comes with all BAM files of one sample cohort, but not with another (but same sample design and workflow used). Rerunning the workflow doesn't help... > > > I would be very thankful for every kind of help! > > > Best, > Sebastian > > Helmholtz Zentrum M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 > > > > ------------------------------ > > Message: 2 > Date: Fri, 29 Nov 2013 09:42:42 -0500 > From: Jim Robinson <jrobinso(a)broadinstitute.org> > To: "Vosberg, Sebastian" <sebastian.vosberg(a)helmholtz-muenchen.de>, > "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> > Subject: Re: [galaxy-user] Problem loading BAM into IGV browser - > invalid GZIP header error message > Message-ID: <5298A7E2.7000908(a)broadinstitute.org> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Sebastian, > > Is it possible to share an example bam that exhibits this problem on a > Galaxy server I can reach? Also, which version of IGV are you using > (select Help > About... to see the version). > > -- Jim > >> Dear all, >> >> >> sometimes I encouter a problem trying to load BAM files directly from Galaxy into the IGV browser. First I am starting the IGV browser locally, then clicking on the appropriate BAM file and on "display with IGV _local_" in Galaxy. In most cases it works, but for some reasons not with specific files. The error message says >> >> "Error loading http://_URL-to-file_/galaxy_example.bam: An error occured while accessing http://_URL-to-file_/galaxy_example.bam >> Invalid GZIP header" >> >> What does it mean? And why am I able to download the BAM file and load it from HDD into the IGV? >> The problem comes with all BAM files of one sample cohort, but not with another (but same sample design and workflow used). Rerunning the workflow doesn't help... >> >> >> I would be very thankful for every kind of help! >> >> >> Best, >> Sebastian >> >> Helmholtz Zentrum M?nchen >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> Ingolst?dter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess, Dr. Nikolaus Blum, Dr. Alfons Enhsen >> Registergericht: Amtsgericht M?nchen HRB 6466 >> USt-IdNr: DE 129521671 >> >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > > ------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > End of galaxy-user Digest, Vol 89, Issue 25 > ******************************************* -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

2 1

ChIP-Seq Normalization to total number of reads
by Wooi Lim 02 Dec '13

02 Dec '13

Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datasets that I want to compare after normalizing each of them to their respective inputs, and these 2 datasets have very different number of reads to start with, is there a way to first normalize each dataset to total number of reads in Galaxy? Thanks. Your help is very much appreciated. Catheryn

2 1

December 2013 Galaxy Update
by Dave Clements 02 Dec '13

02 Dec '13

1 0