Closed ac-simpson closed 1 year ago
Thank you for your report! This is a known problem related to third party operations and the fix will be provided in the next release, in December.
The workaround is to avoid using literature references in your input submol.yaml
file by removing publications:
section.
The workaround is to avoid using literature references in your input submol.yaml file by removing publications: section
I have added a somewhat simpler workaround option by modifying, temporarily, out test case to eliminate aforementioned publications:
section, so you can, if you want, wipe out existing installation and reinstall PGAPx with new test data....
Hi Azat, thanks very much. Unfortunately when I deleted pgap and tried to reinstall (Which I did successfully 5 or 6 times yesterday) the installation is failing every time. I have tried both on our ubuntu server and on my own laptop (Macbook Pro). Specifically,
ERROR: Failed to extract tarball; to install manually, try something like:
curl -OLC - https://s3.amazonaws.com/pgap-data/test_genomes-2022-10-03.build6384.tgz
tar xvf test_genomes-2022-10-03.build6384.tgz
I can't tell if anything else is going wrong.
Hmm... Looks like AWS told me a lie by telling me that this tarball is Public....
I got help to fix this in place. Permissions are now for public, feel free to retry.
Success! Well, someone is hogging our whole server so I started the process on my laptop - and it actually started the script instead of erroring out. Thanks!
Problem After running the installation as described in Quick Start, running the pipeline on the MG37 test genome produces "PGAP failed, docker exited with rc = 1". Running the test genome with "--debug" output is pasted below. Getting the line "Error: (802.5) CObjectOStream: error at line 126: Seq-entry.seq.descr.E.pub.pub.E: cannot write empty choice terminate called after throwing an instance of 'ncbi::CSerialException' " I see that someone else had this issue back in July but the solution was to update the program - and as far as I can tell I am running the latest version. Thanks!
Software versions: