- galaxy-user - lists.galaxyproject.org

Error "out of memory" when trying to retrieve output
by Delong, Zhou 30 Aug '13

30 Aug '13

Hello, I wanted to download the accepted junction .bam file from tophat output of my local instance and I get an "out of memory" error. When I examine the server via command line, I found that a python process used by galaxy occupied more than 80% of total memory (on the virtual machine with 10G of RAM).. I tried curl command to retrieve the datafile after rebooted the virtual machine, and python is activated again and used up all the memory. The bam is around 20G of size, but I never had this kind of problem with other tophat analyses before on my local instance although they are of the same size. The discription on the web mentioned some .dat files that I manage to find on the disk, but not the bam. Can anyone explain what python is doing and how can I solve this please? Thanks, Delong

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Question about expression in Galaxy tools
by 师云 29 Aug '13

29 Aug '13

Hello everyone, I found regular expression could be available in the tool (filter and sort) ->Filter. I wonder whether it could be the same in the tool (Text Manipulation) ->Compute. I have checked that the fuction "len(c4.split('_'))" would return error. So, could anyone tell me if it was possible like this? The file A: chr1 10 40 NM_1234_exon_1 chr2 50 70 NM_1234_exon_2 Change the file A to the file B such as: chr1 10 40 NM_1234 chr2 50 70 NM_1234 May it is useless in the example. But the way could solve problems I met.

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problem with bowtie
by Law, Michael J. 29 Aug '13

29 Aug '13

Hello, I am completely new to using galaxy. I have a quick question. I have uploaded my fastq files generated from my experiment for alignments using bowtie. I try to set up the alignment, only to receive the error message that I don't have any sequences with ASCII encoded quality scores. However, when I contact my sequencing facility, they say that the scores are present in the files and that it may be an issue with galaxy. Any help you can provide would be appreciated! Thanks, Mike Michael Law lawmj(a)rowan.edu<mailto:lawmj@rowan.edu>

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exome-capture sequencing analysis tools?
by Yan He 29 Aug '13

29 Aug '13

Hi Jen and other Galaxy-users, I am working on exome-capture sequencing with NGS. I am wondering if there is a tool to identify SNPs on Galaxy? I would like to get SNP information (position and allele frequency ) for each gene. Any information is highly appreciated! Thanks! Best wishes, Yan

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How to extract geneID from pileup file?
by Yan He 29 Aug '13

29 Aug '13

Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. I did some analysis using Galaxy. First, mapping to the genome with Bowtie. Second, identify SNPs using MPileup in SAMtools. When I got the pileup file, the SNP information is in which chromosome and what position. I would like to focus on the SNPs within genes. How could I extract the SNP information for each genes (SNP position, coverage)? Is there a tool in Galaxy to fulfill this? Any help is highly appreciated! Best wishes, Yan

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Tophat2 not working?
by Delong, Zhou 29 Aug '13

29 Aug '13

Hello, I've been trying tophat 2 on the public server since last week but I don't get any results. I got one empty output for " the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error." one error with " Unable to queue job for execution. Resubmitting the job may succeed." and one empty output with no error message. It seems that tophat 2 is new on the server, has anyone run it with success yet? Thanks, Delong

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CloudMan console not responding
by Deniz Erezyilmaz 29 Aug '13

29 Aug '13

Over the past couple weeks I have had multiple problems using the CloudMan/AWS using a custom pipeline, and I have been unable to complete an instance while racking up large charges from Amazon. There have been three types of problems: 1) Autoscaling and manual changes to the nodes are not showing. Although the EC2 console shows that they are active, the Cloudman console does not, and the performance of the instance suggests that they have not been activated. 2) Share string is not loading. 3) Disk will not resize. Here again, the change appears on the EC2 console, but not on the Cloudman console. The fact that I am unable to load large files suggests that the disk is truly not resized. It seems to me that there is some disconnect between Amazon and Galaxy. Thanks, Deniz

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Galaxy Tool Version Question
by Nixon, Scott Evan 28 Aug '13

28 Aug '13

To Whom it May Concern, I was trying to find the version information regarding certain RNA-Seq analysis (Tophat, Tophat2, Cufflinks), and have had difficulty finding the versions for either Tophat instance. Is there a way to find out what version of Tophat is being used? Thank you for your time, Scott Nixon

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Uploading files to Cloudman by FTP
by Anto Praveen Rajkumar Rajamani 28 Aug '13

28 Aug '13

Hello, I have started a new cloudman instance. Now, I am trying to upload my fastq files to FTP server using Filezilla. The upload file page instructs "To upload some files, log in to the FTP server at localhost using your Galaxy credentials (email address and password)". I typed my ec2... address as the host and entered my Galaxy registered email address and password. Filezilla connects to 220-Galaxy Cloudman FTP but then rejects my password and displays "Could not connect to server". Should I try a different host name? Where do I go wrong? Kindly help me to solve this problem. Thanking you in advance. Best wishes, Anto

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Connecting to new Galaxy Cloudman by FTP
by Mohammad Heydarian 27 Aug '13

27 Aug '13

Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch<http://usegalaxy.org/cloudlaunch> and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Cheers, Mo Heydarian

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