I've got a workflow that uses the old samtools mpileup (v0.0.1) on the main galaxy instance. The next step has been stalling due to metadata not being autodetected in the subsequent dataset. It seems to be happening regardless of the input .bam file. Is this a problem with galaxy? The workflow has worked in the past, probably last time about a month ago.
Thanks!
I am experiencing this as well. The error message:
"12 MPileup on data 7 and data 48 (log)
An error occurred setting the metadata for this dataset
Set it manually or retry auto-detection"
using "toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1"
Thank you
Hi Can I ask in your output files vcf or bcf files? Thanks Guy
The output for this step is .bcf, but the specific file that receives the error message is the log file associated with the .bcf.
Thanks for the info I get the same error on both usegalaxy.org and a cloudman instance regardless of what version of mpileup I use ( I tried 0.0.01, 0.0.02 and 2.0). But I have found a galaxy instance where everything works. So I suspect this is related to a recent galaxy update.
By the way bcftools viewer is installed
Hopefully somebody will be able to help with this.
I deleted my comment
HI I have the same problem but no resolution yet
see
Cannot set metadata on .bcf output from mpileup
I'd like to clarify this problem - it's definitely only a metadata problem, as I can cancel the step after the mpileup, resolve the metadata, then run the subsequent step successfully. Unfortunately this is an early step in a very long workflow, so restarting each step by hand would be quite unwieldy.