[galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)
Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: *Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main # ERROR -- # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): # ERROR The invalid argume *Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach* * ___ 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] Galaxy main not running jobs..
On Jun 16, 2012, at 7:38 PM, Jayaraman, Shyam wrote: Hi, My username is shyamsundar19...@gmail.com Galaxy main is not running jobs since today morning. They stay queued (gray) forever. I deleted and then re queued them twice. Still nothing.. Is the server down or is something wrong with my account?? Hi Shyam, There was a problem with our cluster scheduler that was resolved on Saturday night. Please let us know if you still have problems running jobs. --nate Kindly advice. Shyam S Jayaraman MD Staff Research Associate Division of Dermatology LABioMed Research Institute CA ___ 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] jobs not running on main server
On Jun 16, 2012, at 7:31 PM, Jacob Musser wrote: Hello, I uploaded a couple small files via ftp to do some basic text manipulation on them in the main galaxy server. I have queued up several jobs (including just importing the files I uploaded into a history) but after two hours of waiting they are still gray and waiting to run. I have been using galaxy regularly lately and have never had to wait very long for a job to start running (usually a matter of seconds). I am not above my quota so this is not the problem. Is there something else I need to do or is there a problem with the servers that would explain why jobs aren't being run? Hi Jake, There was a problem with our cluster scheduler that was resolved on Saturday night. Please let us know if you still have problems running jobs. --nate All the best, Jake ___ 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] Reference genome , fasta with or without gene feature
Hello Ateeq, Custom reference genomes are loaded in FASTA format. Help for preparing the data is in our wiki: http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome http://wiki.g2.bx.psu.edu/Learn/CustomGenomes Best, Jen Galaxy team On 6/14/12 9:15 AM, Ateequr Rehman wrote: Dear All I am analysing bacterial RNA seq (illumina). as my reference genome is not in galaxy. so i need to downlaoded the reference genome from NCBI and upload to my history Should i use reference genome with gene features or single fasta file with out any annotation information. even after download should i need to modify or it should be used as it is. Thanks in advance Ateeq ___ 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] FTP Error 530 Sorry, the maximum number of clients (3) for this user are already connected.
Hello , Are you still having trouble with FTP to main? If so, please try loading data with just a single FTP connection. When using FTP to upload files, multiple files can be uploaded through any individual FTP session between your desktop and Galaxy main. If the connections does break (and there are partially transferred files), reestablish the connection with that same FTP tool window ( FileZilla or Cyberduck ) and resume the upload. http://wiki.g2.bx.psu.edu/FTPUpload Hopefully this problem has been resolved or this helps, Jen Galaxy team On 6/14/12 1:18 PM, Christopher M. Weber wrote: Hello, I have been unable to get a solid FTP connection to main.g2.bx.psu.edu for ~24hrs. Two things have occurred: 1) I get the error 530 Sorry, the maximum number of clients (3) for this user are already connected or 2) when finally connected, some files fail during transfer with 'incorrect password' while others continue uploading and eventually the entire connection is lost where attempts to reconnect give the 530 error in situation 1. To troubleshoot, I have tried all suggestions through FileZilla and Cyberduck, essentially limiting number of connections and disabling all before connecting, to no avail. It seems likely that this might be a server issue. Any insight is appreciated. ___ 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] generate pileup not working?
Hello Lilach, Please try running pileup on the original BWA output - (SAM is an OK input with this tool) and let us know if you continue to have problems. Hopefully this helps, Jen Galaxy team // On 6/14/12 1:36 PM, Lilach Friedman wrote: Hi, I am trying to do variants call with generate pileup. My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use Generate pileup https://main.g2.bx.psu.edu/tool_runner?tool_id=sam_pileup from BAM dataset However, it does not work, and I get the error message: 114: Generate pileup on data 97: converted pileup 0 bytes An error occurred running this job: /Samtools Version: 0.1.16 (r963:234) Error running Samtools pileup tool Floating point exception/ Did I do anything wrong, or is it a bug? The parameters are copied below. Thanks, Lilach The parameters are: Tool: Generate pileup Name: Generate pileup on data 97: converted pileup Created:Jun 14, 2012 Filesize: 0 bytes Dbkey: hg_g1k_v37 Format: tabular Tool Version: Tool Standard Output: stdout https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stdout Tool Standard Error: stderr https://main.g2.bx.psu.edu/datasets/d038161e3fe9072e/stderr Input Parameter Value Conditional (refOrHistory) 0 Select the BAM file to generate the pileup file for 97: SAM-to-BAM on data 94: converted BAM Whether or not to print the mapping quality as the last column Do not print the mapping quality as the last column Whether or not to print only output pileup lines containing indels Print all lines Where to cap mapping quality60 Conditional (c) 1 Theta parameter (error dependency coefficient) in the MAQ consensus calling model 0.85 Number of haplotypes in the sample 2 Expected fraction of differences between a pair of haplotypes 0.001 Phred probability of an indel in sequencing/prep40 ___ 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] Problem with Depth of Coverage on BAM files (GATK tools)
Hi Lilach, The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run. UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 http://www.ncbi.nlm.nih.gov/genome/assembly/2758/ with UCSC hg19 http://genome.ucsc.edu for an explanation. Reference genomes must be /exact/ in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. Good luck with the re-run! Jen Galaxy team On 6/18/12 4:42 AM, Lilach Friedman wrote: Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: /Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main # ERROR -- # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): # ERROR The invalid argume /Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach/ / ___ 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] Problem with Depth of Coverage on BAM files (GATK tools)
I'm curious what is this genome called 'hg_g1k_v37' and how does it correspond to NCBI GRCh37 which is identical to UCSC hg19 ? --Hiram Jennifer Jackson wrote: UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 http://www.ncbi.nlm.nih.gov/genome/assembly/2758/ with UCSC hg19 http://genome.ucsc.edu for an explanation. Reference genomes must be /exact/ in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. ___ 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] Problem with Depth of Coverage on BAM files (GATK tools)
If hg_g1K_v37 == 1000 Genomes version of GRCh37 then it is the GRCh37 Primary assembly + a decoy sequence to try to soak up off target reads. The chromosome coordinates are the same but the sequences included in the packages are different. Here is the description from the 1000 Genomes site: http://www.1000genomes.org/category/assembly Deanna On 6/18/12 3:30 PM, Hiram Clawson hi...@soe.ucsc.edu wrote: I'm curious what is this genome called 'hg_g1k_v37' and how does it correspond to NCBI GRCh37 which is identical to UCSC hg19 ? --Hiram Jennifer Jackson wrote: UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 http://www.ncbi.nlm.nih.gov/genome/assembly/2758/ with UCSC hg19 http://genome.ucsc.edu for an explanation. Reference genomes must be /exact/ in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. ___ 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/
