❗❗❗ Downtime 4/24-5/2 2023

[kmoad]

The datacenter hosting run.opencravat.org and the OpenCRAVAT module store will be down from Monday 4/24 to Monday 5/1 for maintenance on their cooling system.

While run.opencravat.org will be unavailable during that window, users with local installations can continue working by configuring their system to download modules from the AWS OpenData mirror.

Additionally, you can download finished jobs from run.opencravat.org to view locally.

• Click the row in the jobs table
• Click the "DB" button to download the job sqlite result
• On a system with OpenCRAVAT installed, run oc gui result-file-name.sqlite

We apologize for the inconvenience this causes. Further updates will be posted to this thread and to our twitter.

[katelynmullen]

I cannot run OC from the command line yet. It successfully runs the converter, but then hangs indefinitely when running the gene mapper. Can you replicate this on your end? I am trying to run a tiny file of only 3 lines.

s_MPAM18_qcf_cravat.xlsx

[skanderson]

@katelynmullen

I was not able to replicate this problem just now; I saved that file as a tsv, then I ran oc run s_MPAM18_qcf_cravat.tsv -a clinvar -l hg38 with no errors.

Are you seeing files named s_MPAM18_qcf_cravat.xlsx.err and s_MPAM18_qcf_cravat.xlsx.log in the directory you ran the job? The contents of those might help us find the issue.

You might also want to run oc module update to make sure all your modules are up to date.

[katelynmullen]

I also run this as a .tsv, I just had to convert to xlsx to upload to Github

I am running as follows:

oc run /res/iacobuzc/share/Katelyn/opencravat/big_four_rescue/MPAM18/s_MPAM18_qcf_cravat.tsv -l hg19 -t text -d /res/iacobuzc/share/Katelyn/opencravat/big_four_rescue/MPAM18 -a aloft biogrid cadd cancer_genome_interpreter cancer_hotspots cgc chasmplus chasmplus_PAAD civic clinvar cosmic fathmm gnomad3 go mutpanning oncokb polyphen2 revel

Nothing is writing to the .err file. Attaching the log file.

I ran oc module update to make sure everything is up to date, but to no avail. s_MPAM18_qcf_cravat.tsv.log

[kmoad]

It's run ok on my end as well. You could try reinstalling mapper. Also, what version of oc? Run oc version.

To reinstall mapper

oc module uninstall hg38
oc module install hg38

[katelynmullen]

I tried reinstalling mapper and oc in general and neither worked. I tried a test again this morning with the one patient I sent you and it successfully ran in 43 seconds. However, when I tried to cat a file of commands for 88 patients, gene mapper stalled. Then I tried to rerun the single patient again, but the gene mapper continued to stall.

[kmoad]

Closing to switch to https://github.com/KarchinLab/open-cravat/issues/153