InterProScan proxy warning
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Entering edit mode
14 months ago
Sergio • 0

Hi,

I am using InterProScan-5.51-85.0 to annotate ~20K proteins from a Poceae plant. I use for it the next command:

/data/software/interproscan-5.51-85.0/interproscan.sh \
    --output-dir /data/work/poceae/annotation_result \
    --input /data/triticum/genomes/poceae/poceae_annotation_200916/annotationInterPROScan/poceaev2.1_annotation_200916_HC_pep.valid.00.fasta \
    --appl PFAM,PANTHER \
    --formats TSV \
    --iprlookup \
    --goterms \
    --pathways \
    --seqtype p

The computer is behind a firewall so I need a proxy to reach outside. To do that, I have modified the file interproscan.properties as follows:

#proxy set up
precalculated.match.lookup.service.proxy.host=proxy.satd.uma.es
precalculated.match.lookup.service.proxy.port=3128

In addition, in the same session of Linux, I have exported the corresponding proxy variables:

export HTTP_PROXY=http://proxy.satd.uma.es:3128 
export HTTPS_PROXY=http://proxy.satd.uma.es:3128 
export FTP_PROXY=http://proxy.satd.uma.es:3128

Unfortunately, no matter how many proteins contains the fasta file, I obtain the next messages again and again:

2021-05-06 12:22:01,980 [Thread-10] [uk.ac.ebi.interpro.scan.precalc.client.MatchHttpClient:142] WARN - HTTP Proxy Warning: this run is configured to use an http proxy, InterProscan is however unable to handle this properly.

2021-05-06 12:22:01,980 [Thread-6] [uk.ac.ebi.interpro.scan.precalc.client.MatchHttpClient:142] WARN - HTTP Proxy Warning: this run is configured to use an http proxy, InterProscan is however unable to handle this properly.

Though it is a Warning and not an Error, it is clear that the lookup is not working smoothly. Is the program correctly connecting to the lookup service? Am I obtaining a good annotation for each of my proteins? What is the actual problem and how to remove it?

Thank you in advance!

linux lookup http • 549 views
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Can you check some of the suggestions in https://github.com/ebi-pf-team/interproscan/issues/68? Also make sure that you have the latest version of InterProScan since manual indicates that the service they run is the latest and is thus only compatible with latest version of InterProScan.

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Entering edit mode

Thank you. Sentence ./interproscan.sh -i test_all_appl.fasta -f tsv --appl PFAM,PANTHER -dp taken from the link you provide (adding only requested analysis) seems to work fine.

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Entering edit mode

Why not disable the lookup service and just run the local scans?

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Entering edit mode

Thank you. That option (-dp) may be a workaround. However, it does not resolve the problem and it does not clarify its origin.

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