philosopher
philosopher copied to clipboard
`philosopher-v4.5.1-RC5 database --id UP000299084,UP000504605,UP000030684` does not work anymore
Describe the bug
philosopher-v4.5.1-RC5 database --id UP000299084,UP000504605,UP000030684
should download the FASTAs
To Reproduce
#!/bin/bash
set -euxo pipefail
TMPDIR=$PWD
TMP=$TMPDIR
TEMP=$TMPDIR
export TMPDIR TMP TEMP
export JAVA_OPTS=-Djava.io.tmpdir=$PWD
PHILOSOPHER=/usr/local/nesvilab/philosopher_v4.5.1/philosopher-v4.5.1-RC5
${PHILOSOPHER} version
${PHILOSOPHER} workspace --temp $PWD
${PHILOSOPHER} workspace --clean
${PHILOSOPHER} workspace --init
${PHILOSOPHER} database --id UP000299084,UP000504605,UP000030684
Expected behavior
it should work as in the past (June 13th)
[bfabric@fgcz-c-073:WU278439]$ grep "^>" 2022-06-13-decoys-UP000299084-UP000504605-UP000030684.fas |wc -l
173536
Please complete the following information:
cpanse@fgcz-c-073:/scratch/cpanse/philosopher > ${PHILOSOPHER} version
INFO[12:00:32] Current Philosopher build and version build=202207271218 version=v4.5.1
cpanse@fgcz-c-073:/scratch/cpanse/philosopher > uname -a
Linux fgcz-c-073 5.4.121-0504121-generic #202105220633 SMP Sat May 22 10:38:55 UTC 2021 x86_64 GNU/Linux
Additional context
please let me know if I can help you in any way. thanks!
Apparently, you stumbled on another undocumented API break from UniProt. This time I don't have a quick to fix it because I still don't know how to handle this. For now, you'll have to grab the FASTA from the website, sorry.