Hi may i have a quick check regarding fastqc? It seems that it is taking forever to run for the past few days, especially in a workflow. Would appreciate it anyone can take a look. Thanks !
Hi,
yes, we noticed this already. @bjoern.gruening any new insights on this?
@zschong have you tried running falco instead? Also have you tried usegalaxy.org on the same inputs? Maybe we can figure out what’s wrong together.
Hi @wm75 & @bjoern.gruening ,
Thank you for helping out!
I did try falco moments ago and it looks fine. And the problems seem to be specific to galaxy euro as fastqc runs well in galaxy.org.
@zschong great! That’s helpful information and falco is our recommendation over fastqc anyway nowadays and a drop-in, more efficient replacement.
Nevertheless, we will debug the fastqc issue, of course, though maybe only on Monday.
@wm75 Yup thanks for the falco heads-up. No worries pls take your time to debug fastqc. thanks and have a great week ahead!
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In the end, it was an NFS (shared-file-system) locking issue with some font-cache in FATQC.
I tried to recover all stuck jobs. Hope yours are now running or are finished. If not please restart them.
Happy research!
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Will go and take a look later. Appreciate your help and thanks everyone