Code for building InterProScan docker container and supporting scripts
Home Page: https://agbase-docs.readthedocs.io/en/latest/interproscan/intro.html
License: Creative Commons Zero v1.0 Universal
Documentation for the version of InterProScan is hosted by ReadtheDocs: https://agbase-docs.readthedocs.io/en/latest/.
The -cyverse directories contains files for the DE app with file paths optimized for Cyverse environment.
Missing opening tag
surya@malus:~/work/NAL/i5k_first_10_set/APLA.faa/def-45-80-APLA_full$ xmllint APLA.xml
APLA.xml:46911: parser error : Extra content at the end of the document
<protein>
^
It looks like the merging skips the opening tag
<?xml version="1.0" encoding="UTF-8"?><protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5" interproscan-version="5.45-80.0">
So we have a bunch of dangling </protein-matches> tags
Each parallel job gets all CPUs passed from the command line
InterProScan/5.36-75/iprs_wrapper.sh
Line 154 in 0d1eae9
InterProScan/5.41-78/Dockerfile
Line 68 in 0647e28
Breaks all post processing.
Test on BTI Debian and Ubuntu servers. Mac laptop
Hi there,
I try to follow along (https://agbase-docs.readthedocs.io/en/latest/interproscan/using_iprs_cmd.html#running-interproscan-with-singularity-or-apptainer-on-hpc) and encounter this error:
"ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back."
See more details at
Any idea how I could make this work?
Thanks a lot,
Liyong
InterProScan/5.41-78/iprs_wrapper.sh
Line 171 in 1f716b7
Rename or halt run
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