User: skasowitz

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skasowitz70
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Posts by skasowitz

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Comment: C: Galaxy space required
... If you are working on usegalaxy.org you are limited to 250 GB for your account. For other installations, such as a local install, you will need to talk to whoever administers it about increasing disk space quotas. You can possibly free up space by permanently deleting some datasets that you don't n ...
written 2.5 years ago by skasowitz70
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CummerBund Memory Allocation Error on usegalaxy.org
... After working for at least an hour, a CummerBund job on usegalaxy failed with the following error This job was terminated because it used more memory than it was allocated. Is there a different way I should launch this job? ...
cummerbund written 2.5 years ago by skasowitz70 • updated 2.5 years ago by Jennifer Hillman Jackson25k
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Comment: C: Merging BAM files: bamtools not found
... Thank you and Happy New Year! ...
written 2.5 years ago by skasowitz70
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Merging BAM files: bamtools not found
... I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned sequences from each lane into a single BAM file. When I attempt to use bamtools on usegalaxy.org I am receiving the following error: Fatal error: Exit code 127 () /galaxy-repl/main/jobdir/011/351/11351255/g ...
galaxy bamtools written 2.6 years ago by skasowitz70 • updated 12 months ago by cpreviti0
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Comment: C: Merge BAM files
... When I try to merge BAM files I receive the following error Fatal error: Exit code 127 () /galaxy-repl/main/jobdir/011/348/11348779/galaxy_11348779.sh: line 42: bamtools: command not found ...
written 2.6 years ago by skasowitz70
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Comment: C: No space left on device
... Thanks for the update! I have started some QC jobs and will try mapping again tonight. Everything looks good so far (no immediate errors). ...
written 2.6 years ago by skasowitz70
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Comment: A: Problem concatenating different lanes
... Hi iachaim This is a problem people are seeing with all sorts of tools and also loading data. You can see some other reports over on this thread. Unfortunately we currently have no information about what is wrong as the thread is primarily users sharing their similar problems. Still it might be wor ...
written 2.6 years ago by skasowitz70
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Comment: C: No space left on device
... I was able to upload several files by through the web interface yesterday at around 18:30 UTC. [edit: All files were compressed fastq files in the range of 1.5-2.0GB compressed.] No jobs seem able to start up beyond this, regardless of data quota. I have no retried the mapping that originally genera ...
written 2.6 years ago by skasowitz70
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Answer: A: No space left on device
... Some Tophat mapping jobs I had started about 4 hours ago all began failing over the past hour with various errors. They had all finished mapping left and right sequences. Some other jobs in the queue then failed to begin returning "No space left on device" errors. I encountered a similar problem as  ...
written 2.6 years ago by skasowitz70

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Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: No space left on device

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