[galaxy-user] Job waiting to RUN
Dear Administrators Since yesterady my bowtie alignment is waiting to run, message is just, job waiting to run could you plesae see the problem Thank you Ateequr Rehman ___ 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/
[galaxy-user] wig to bigwig error
Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tried to convert it to a bigwig file. The dataset came from Bing Ren's lab, and its GEO record is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344 The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8 rather than mm9 based on the GEO record: 49: GSM560344_03112009_313D2AAXX_B7.wi ~960,000 lines format: wig, database: mm8 Info: uploaded wig file display at UCSC main The details for this upload are as follows: Tool: Upload File Name: GSM560344_03112009_313D2AAXX_B7.wi Created:Dec 08, 2011 Filesize: 12.1 Mb Dbkey: mm8 Format: wig Tool Version: Tool Standard Output: stdout Tool Standard Error:stderr Input Parameter Value File Format auto Genome Conditional (files_metadata)32 Inheritance Chain GSM560344_03112009_313D2AAXX_B7.wi The wig-to-bigWig conversion on data 49 (using the wig to bigwig conversion tool in the convert formats toolbox) was run on March 21, 2012 and gave the following error: 77: Wig-to-bigWig on data 49 0 bytes An error occurred running this job:line 152351 of stdin: chromosome chr13 has 120614378 bases, but item ends at 120614600 line 298005 of stdin: chromosome chr17 has 95177420 bases, but item ends at 95177625 line 325066 of stdin: chromosome chr16 has 98252459 bases, but item ends at 9825252 The details for this operation are as follows: Tool: Wig-to-bigWig Name: Wig-to-bigWig on data 49 Created:Mar 21, 2012 Filesize: 0 bytes Dbkey: mm8 Format: bigwig Tool Version: Tool Standard Output: stdout Tool Standard Error:stderr Input Parameter Value Convert 49: GSM560344_03112009_313D2AAXX_B7.wi Conditional (settings) 1 Items to bundle in r-tree 256 Data points bundled at lowest level 1024 Clip chromosome positions True Do not use compression True Inheritance Chain Wig-to-bigWig on data 49 I gather that the chromosome ends are not being snipped off, even though I toggle this option on the galaxy conversion tool. And I know it's doing something, because if I toggle that option off, I get an error that includes broken pipe and simply aborts. I apologize for knowing so little about the bioinformatics involved here. And I'm sure I've overlooked something that is likely obvious to others and/or failed to provide some critical bit of info in this email. But any help would be greatly appreciated. Thanks, Mike ___ 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/
Re: [galaxy-user] History not accessible
Hi Luciano, The '228Gb' number can take some time to update, but this should be be a most few hours, not an entire day. To remove datasets from a history permanently (and remove them from disk) you will need to do two things: 1 - delete by clicking on the X for those datasets 2 - use 'Options - 'Purge deleted datasets' Within an individual history, using 'Show Hidden Datasets' is a way to locate datasets similar to Show Deleted Datasets' (hidden datasets can be produced by workflows). Hidden datasets are often intermediate data that is not needed and could possibly be deleted/purged as well. For histories, any ever created/imported by your account will be in your 'Saved Histories' list (for now, there is no expiration date). Therese are automatically saved once you are logged in and do not require a special name. Is isn't clear if you think one is missing or not. Do you think a history was deleted by accident? If so, it can be viewed under Saved Histories by using 'Advanced search' with the option 'all'. Histories of status 'delete' can be 'undeleted' and moved back to 'active' status, histories of status 'deleted permanently' cannot be recovered. This wiki screencast has more details: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently Hopefully this helps, but please write back if you need more assistance, Jen Galaxy team On 4/13/12 6:07 AM, Luciano Cosme wrote: Hi, After I uploaded a couple files yesterday, I hit the storage limit (250Gb), then I deleted 3 datasets from my history and now I can't see anything in that history. It still says that I am using 228Gb, but I can only access one history with ~98Gb. I try to use show deleted datasets and it still not showing. The history that I was using disappeared. When I use saved datasets I only see one history. I was logged as ento.purch...@gmail.com mailto:ento.purch...@gmail.com Thank you. Luciano ___ 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/ ___ 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/
Re: [galaxy-user] Job waiting to RUN
Hi Ateequr, We can let you know that the public main Galaxy instance is very busy right now and this is the cause for the delay. A cloud instance many be a solution for your or others reading this post. Help to get started is in this wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud Take care, Jen Galaxy team On 4/13/12 2:38 AM, Ateeq ur Rehman wrote: Dear Administrators Since yesterady my bowtie alignment is waiting to run, message is just, job waiting to run could you plesae see the problem Thank you Ateequr Rehman http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? Follow *_Rediff Deal ho jaye! http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_cid=rediffmailsignature___cmp=signaturelnk=rediffmailsignaturenewservice=deals_* to get exciting offers in your city everyday. ___ 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/ ___ 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/
Re: [galaxy-user] Alignment coordinates
Hi Erika, Unfortunately, Galaxy does not have a parser tool to transform clustal datatypes into tab-coordinate based files. Sorry we couldn't help! Best, Jen Galaxy team On 4/12/12 8:07 AM, Erika Kruse wrote: Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coordinates of the matching regions? Thank you. Erika ___ 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/ ___ 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/
Re: [galaxy-user] Alignment coordinates
Erika, Although Galaxy doesn't have a suitable mapping tool for fasta format sequences, you can use the Galaxy clustalw tool option to output a fasta format file and then upload that fasta file to the ncbi Blast tool at http://blast.ncbi.nlm.nih.gov/Blast.cgi to find where the sequences align - blast allows mapping of sequences on multiple organisms. I hope this helps in your research On Fri, Apr 13, 2012 at 10:36 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Erika, Unfortunately, Galaxy does not have a parser tool to transform clustal datatypes into tab-coordinate based files. Sorry we couldn't help! Best, Jen Galaxy team On 4/12/12 8:07 AM, Erika Kruse wrote: Hello, I imported a sequence alignment file from clustalw. How can I generate a list of the coordinates of the matching regions? Thank you. Erika ___ 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/ ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-user] wig to bigwig error
Hi Michael, This particular .wig file has a data format problem that is the root cause of the conversion error. Specifically, there is an extra track line in the file. This can be found using unix tools with a grep or in Galaxy with the tool Filter and Sort - Select by matching the pattern track. Ideally this would be corrected and resubmitted by the data author before use, since how/why this was inserted and what impact it has would need to be examined. Since you noticed problems with other GEO files (conversion problems), verifying the .wig format and making any necessary corrections would also be advised. Hopefully this helps! Best, Jen Galaxy team On 4/13/12 6:19 AM, Michael Sikes wrote: Hi, I have hit a brick wall when trying to convert wig files from the GEO to bigwig files. Each time I try (and I have tried many times since October), I get the same error. For example, here is a downloaded wig file, that I assigned to the mouse mm8 genome, and the error I got when I tried to convert it to a bigwig file. The dataset came from Bing Ren's lab, and its GEO record is here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM560344 The wig file was uploaded to Galaxy Dec. 8, 2011, and I assigned mm8 rather than mm9 based on the GEO record: 49: GSM560344_03112009_313D2AAXX_B7.wi https://main.g2.bx.psu.edu/history ~960,000 lines format: wig, database: mm8 Info: uploaded wig file https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/display?to_ext=wighttps://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/show_paramshttps://main.g2.bx.psu.edu/tool_runner/rerun?id=4746000https://main.g2.bx.psu.edu/history https://main.g2.bx.psu.edu/tag/retag?item_id=47465bc44dbd111eitem_class=HistoryDatasetAssociationhttps://main.g2.bx.psu.edu/dataset/annotate?id=47465bc44dbd111e display at UCSC main https://main.g2.bx.psu.edu/datasets/4746000/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm8%26position%3Dchr11%3A3000251-3023451%26hgt.customText%3D%25sdisplay_url=https%3A%2F%2Fmain.g2.bx.psu.edu%2Froot%2Fdisplay_as%3Fid%3D4746000%26display_app%3Ducsc%26authz_method%3Ddisplay_at The details for this upload are as follows: Tool: Upload File Name: GSM560344_03112009_313D2AAXX_B7.wi Created:Dec 08, 2011 Filesize: 12.1 Mb Dbkey: mm8 Format: wig Tool Version: Tool Standard Output: stdout https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/stdout Tool Standard Error:stderr https://main.g2.bx.psu.edu/datasets/47465bc44dbd111e/stderr Input Parameter Value File Format auto Genome Conditional (files_metadata)32 Inheritance Chain GSM560344_03112009_313D2AAXX_B7.wi The wig-to-bigWig conversion on data 49 (using the wig to bigwig conversion tool in the convert formats toolbox) was run on March 21, 2012 and gave the following error: 77: Wig-to-bigWig on data 49 https://main.g2.bx.psu.edu/history 0 bytes An error occurred running this job:/line 152351 of stdin: chromosome chr13 has 120614378 bases, but item ends at 120614600 line 298005 of stdin: chromosome chr17 has 95177420 bases, but item ends at 95177625 line 325066 of stdin: chromosome chr16 has 98252459 bases, but item ends at 9825252/ https://main.g2.bx.psu.edu/dataset/errors?id=6041022https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/show_paramshttps://main.g2.bx.psu.edu/tool_runner/rerun?id=6041022 https://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/display/?preview=Truehttps://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/edithttps://main.g2.bx.psu.edu/datasets/48bd55b0d18aebad/delete?show_deleted_on_refresh=False The details for this operation are as follows: Tool: Wig-to-bigWig Name: Wig-to-bigWig on data 49 Created:Mar 21, 2012 Filesize: 0 bytes Dbkey: mm8 Format: bigwig Tool Version: Tool Standard Output: stdout https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/stdout Tool Standard Error:stderr https://main.g2.bx.psu.edu/datasets/a2b45d5d5a106890/stderr Input Parameter Value Convert 49: GSM560344_03112009_313D2AAXX_B7.wi Conditional (settings) 1 Items to bundle in r-tree 256 Data points bundled at lowest level 1024 Clip chromosome positions True Do not use compression True Inheritance Chain Wig-to-bigWig on data 49 I gather that the chromosome ends are not being snipped off, even though I toggle this option on the galaxy conversion tool. And I know it's doing something, because if I toggle that option off, I get an error that includes broken pipe and simply aborts. I apologize for knowing so little about the bioinformatics involved here. And I'm sure I've overlooked something that is likely obvious to others and/or failed to provide some critical bit of info in this email. But any help would be greatly appreciated. Thanks, Mike ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public
Re: [galaxy-user] Job waiting to RUN
Hi Jen, I am experiencing the same issue (job pending since yesterday) as Ateequr, but not with other tools such as pileup. Are you sure this is due to heavy load, not because of problems with Bowtie tool? It might just take a while for me to figure out how to use your cloud instance. Thanks, Michael -Original Message- From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: Friday, April 13, 2012 9:06 AM To: Ateeq ur Rehman Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Job waiting to RUN Hi Ateequr, We can let you know that the public main Galaxy instance is very busy right now and this is the cause for the delay. A cloud instance many be a solution for your or others reading this post. Help to get started is in this wiki: http://wiki.g2.bx.psu.edu/Admin/Cloud Take care, Jen Galaxy team On 4/13/12 2:38 AM, Ateeq ur Rehman wrote: Dear Administrators Since yesterady my bowtie alignment is waiting to run, message is just, job waiting to run could you plesae see the problem Thank you Ateequr Rehman http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm@Middle? Follow *_Rediff Deal ho jaye! http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_cid=rediffmailsignature___cmp=signaturelnk=rediffmailsignaturenewservice=deals_* to get exciting offers in your city everyday. ___ 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/ ___ 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/ Email Disclaimer: www.stjude.org/emaildisclaimer ___ 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/
Re: [galaxy-user] FASTQ joiner fails to join PE data.
Hello, The FASTQ Joiner tool is currently being updated to work with the newer sequence Id format. The progress of this change can be tracked here: https://bitbucket.org/galaxy/galaxy-central/issue/677/update-joiner-tool-to-work-with-casava-18 Meanwhile, quality filtering can be done on each file independently, then to synch up the two files (in case sequences are lost in one of the files for quality reasons), a work-around method is: - NGS: QC and manipulation - FASTQ to Tabular on both files - Join, Subtract and Group - Join two Datasets on c1 from both files Keep lines of first input that do not join with second input: as yes Keep lines of first input that are incomplete: as no Fill empty columns: as no - NGS: QC and manipulation - Tabular to FASTQ run twice Recreate both FASTQ files from the same tabular file. The same sequence identifier column will be used in both runs. Hopefully this helps until we have the the regular FASTQ manipulation tools updated, Jen Galaxy team On 4/3/12 12:44 PM, meganathan pr wrote: Hi, I have HiSeq2000 paired end sequence data in two separate FASTQ files. I need to filter the low quality scored sequences from my data to have a good assembly. So I decided to join the PE reads and then filter the low quality sequences in Galaxy. To do this first I groomed the data using FASTQ groomer where I kept Sanger as Input FASTQ quality scores type. Then I tried to join the PE sequences using FASTQ joiner. However the FASTQ joiner did not join the PE sequences but only shown the failure Info as follows *FASTQ joiner on data 8 and data 9* 0 bytes format: fastqsanger, database: ? https://main.g2.bx.psu.edu/datasets/d08dd42f0e2ed22b/edit Info: There were 400 known sequence reads not utilized. Joined 0 of 400 read pairs (0.00%). I am a new user and I have no idea where I am going wrong. Please suggest me how to overcome this problem. Thanks. -- ** ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
Re: [galaxy-user] Editing workflows : Server error ?
Hi Sandrine, Would you have time to share one of these workflows that produces a Server error, so that we can examine your exact case and determine the root cause of the problems? To do this, on the Your workflows page, use the pull-down menu to select Share or Publish, generate a share link, and email that back to me directly (not to the entire list). Also sending the exact steps that you know will produce a server error would be appreciated. Thank you for reporting the issue and I will watch for your reply, Best, Jen Galaxy team On 4/13/12 10:50 AM, Sandrine Hughes wrote: Dear all, I didn't use Galaxy for some weeks now. When I tried to edit some of my workflows today I received an error message Server error instead. Is there any problem with the workflow editor or to edit big workflows (40 steps) recently ? It seems that I can only edit workflows with a limited number of steps. Thanks a lot, Sandrine ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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/
