minor bug report - read more link on service alert banner takes me to...
The read more link in the service link just takes me to the portal GUI.
View ArticleWorkflow failing with error: cannot find credentials for RawlsUser
I am launching workflows using the firecloud API (python fiss wrapper). The workflows are being launched within a web application running on Google App Engine. The web app is running under the service...
View Article"Bad output 'covered_bases': For input string: "2672692578""
Hi, Besed on the log files, I think my pipeline is succeeded. But, there is an issue on one of the outputs. I want to attach both the output file and the first line value (Int) in that file to entity...
View ArticleTask JointGenotyping.ImportGVCFs failed with message 10: failed to copy files
Task JointGenotyping.ImportGVCFs failed on joint discovery of 34 exome samples: When I look into the stderr.log file: 08:33:54.012 INFO GenomicsDBImport - Starting batch input file preload 08:33:59.013...
View Articlem2 gatk4 oncotated maf output includes rejected mutations
The oncotated maf output includes many rejected mutations (using the configuration from the public spaces). This is bad practice. The unfiltered VCF (or preferably a tsv) should have these sites but we...
View ArticleGetting an error saying E: command failed: CommandException: No URLs matched:
I have been updating the bismark_wgbs method configuration in aryee-lab/dna-methylation workspace for visualizing the BAM files. BAM files are generated without a problem but when I try to generate BAM...
View Articlehow can I install firecloud on my local server?
Can I install firecloud on my server? Where I can get? Thanks for your help. Best, Leandro
View ArticleCan anyone log in to FireCloud 20 Oct in the morning?
I tried to log into FC this morning and could not log in. I got a message Error loading user information. Please try again later. I tried to log in with both my broad and personal accounts and got the...
View Articlerevive redacted method version
Hi Firecloud, I redacted an old snapshot of a method, but need to revive it. Can someone help me with this? Thank you! Daniel
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How do I make a workspace public?
I see the "Publicly Readable?" check box in my method after clicking the share icon, but i don't see the check box for a workspace I created. How do i make my workspace public?
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Configuration Not compatible warning.
I created method configuration for snapshot 7 of a wdl. When i go to the methods repo click on my method with the latest snapshot (7) and go to the configuration tab there is an incompatibility warning...
View ArticleExport five-dollar-genome-analysis-pipeline to Workspace
When I try to export the Export five-dollar-genome-analysis-pipeline to my Workspace, I am getting the message: You don't have access to any published configurations for this method. The only option...
View Article[Publish] Publish my own WDL including GATK
Hi, I have several tested WDL scripts including some GATK command lines and PUBLIC GATK docker images. Could you please let me know whether I am allowed to pulish them on FC so that more people can...
View ArticleCan there be a rational order to the call in the monitor view?
...or perhaps there is one, but it's beyond me. Here are the calls I see (together, for your enjoyment, the order in which they show up in the timing diagram): {{ 3. CheckBuild 2. dbRsIDsSize_string 6....
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Call QueuedInCromwell, Job Running?
Hi there-- I've been using FireCloud with great success, and just did a preliminary method run on about 275 files using a WDL that I wrote...
View Articlehaplotypecaller_gvcf_gatk4 failed to delocalize files
Hello, I was running haplotypecaller_gvcf_gatk4 for four samples in the same workspace. All but one finished the analysis. Message for the failed sample (all 50 shards) is as the following, Task...
View ArticleFireCloud is very slow
Submitted a job more than an hour ago. JES log hasn't been created yet. Is something causing FireCloud to be slow? Thanks!
View ArticleFuncotator in Mutect2 workflow lacks reference setting and fails to run
Hi, I've just run a clone of the Somatic-SNVs-Indels-GATK4 workspace with run Funcotator set to true. It appears to have failed, looking at the standard error output it would appear that the WDL /...
View ArticleMutect2 workflow bam out fails
Hi I've just run a clone of the Somatic-SNVs-Indels-GATK4 workspace, looking over the output of the WDL in the Monitor section Mutect2.sub_bamout_size has been flagged as failed with Started: reading...
View ArticleAll Out of Credits - Error?
Well, all good things come to an end. My heavy experimentation with FC dwindled my credits in less than a week (oops!) This happened in the middle of a run, which caused everything to error out. After...
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