Interproscan log4j error

usegalaxy.org.au support
1

Hi there,
I was trying to run Interproscan on a fasta of peptides, and got this error:

Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Duser.home=/mnt/tmp/job_working_directory/006/694/6694561/home
log4j:WARN No appenders could be found for logger (org.apache.activemq.broker.BrokerService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See Apache log4j 1.2 - Frequently Asked Technical Questions for more info.

Command line:
mkdir -p $HOME/.interproscan-5 && sed ā€˜s|^(data.directory=).*$|\1/mnt/custom-indices/interproscan/5.59-91.0/data|ā€™ $(dirname $(readlink -f $(command -v interproscan.sh)))/interproscan.properties > $HOME/.interproscan-5/interproscan.properties && export _JAVA_OPTIONS=-Duser.home=$HOME && interproscan.sh -dp --input ā€˜/mnt/user-data-7/014/533/dataset_14533041.datā€™ --seqtype p -f TSV --applications TIGRFAM,FunFam,SFLD,SUPERFAMILY,PANTHER,Gene3D,Hamap,PrositeProfiles,Coils,SMART,CDD,PRINTS,PIRSR,PrositePatterns,AntiFam,Pfam,MobiDBLite,PIRSF,Phobius,SignalP_EUK,TMHMM --tempdir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --pathways --goterms --cpu ${GALAXY_SLOTS:-4} --output-file-base ā€˜outputā€™

Tool Standard Output:
03/07/2023 18:03:56:933 Welcome to InterProScan-5.59-91.0
03/07/2023 18:03:56:935 Running InterProScan v5 in STANDALONE modeā€¦ on Linux
Invalid input specified for -appl/ā€“applications parameter:
Analysis Phobius does not exist or is deactivated.
Analysis TMHMM does not exist or is deactivated.
Analysis SignalP_EUK does not exist or is deactivated.

Tool Standard Error:
Picked up _JAVA_OPTIONS: -Duser.home=/mnt/tmp/job_working_directory/006/694/6694561/home
log4j:WARN No appenders could be found for logger (org.apache.activemq.broker.BrokerService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See Apache log4j 1.2 - Frequently Asked Technical Questions for more info.

2

Hi @Tyler_Coale

That looks like a dependency problem but could also be a job that died, or failed for some transient cluster reason (a rerun would fix the latter). Inputs are another factor to consider.

What happens if you run this with fewer Applications? Start by excluding these. The tool is reporting that the input is a mismatch.

Iā€™m not even sure how those were even selected at UseGalaxy.org.au. The most current version of the tool filters Applications based on the Protein versus DNA toggle at the top of the form, and those listed in the error message are no longer included/available for either.

If you need more help, please share more details. Troubleshooting errors

3

Hi @Tyler_Coale
you activated three ā€œnon-commercialā€ modules that are not available on Galaxy Australia. We cannot guarantee non-commercial use of software.
Do not use these modules.
Kind regards,
Igor

1 Like