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ebi-pf-team / interproscan

Genome-scale protein function classification
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Deactivated analyses #368

Closed Paolopab closed 1 week ago

Paolopab commented 2 months ago

Hello everyone,

After installing InterProScan and placing Phobius, SignalP, and TMHMM in the folders required by InterPro, the following analyses still appear to be disabled:

Deactivated analyses: SignalP_GRAM_NEGATIVE (4.1) : Analysis SignalP_GRAM_NEGATIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp TMHMM (2.0c) : Analysis TMHMM is deactivated, because the resources expected at the following paths do not exist: bin/tmhmm/2.0c/decodeanhmm, data/tmhmm/2.0c/TMHMM2.0c.model SignalP_EUK (4.1) : Analysis SignalP_EUK is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp Phobius (1.01) : Analysis Phobius is deactivated, because the resources expected at the following paths do not exist: bin/phobius/1.01/phobius.pl SignalP_GRAM_POSITIVE (4.1) : Analysis SignalP_GRAM_POSITIVE is deactivated, because the resources expected at the following paths do not exist: bin/signalp/4.1/signalp

How can I solve this?

tgrego commented 2 months ago

Hello, can you please confirm the files shown on the error message exist as expected in your InterProscanDir? InterProscanDir/bin/signalp/4.1/signalp InterProscanDir/bin/tmhmm/2.0c/decodeanhmm InterProscanDir/data/tmhmm/2.0c/TMHMM2.0c.model InterProscanDir/bin/phobius/1.01/phobius.pl

Interproscan will need those files in order to activate the analyses.

Paolopab commented 2 months ago

Hello thank you, interproscan-5.68-100.0/bin/signalp/4.1/signalp

interproscan-5.68-100.0/bin/signalp/4.1/signalp$ ls

conversion_utils make_output_files.py predict.py init.py make_sequence_plot.py sequential_model.py main.py model_weights utils.py

interproscan-5.68-100.0/bin/phobius/1.01

interproscan-5.68-100.0/bin/phobius/1.01$ ls

decodeanhmm OPSD_SHEEP phobius.model phobius.pl README decodeanhmm.64bit phobius_install.txt phobius.options Q8TCT8

interproscan-5.68-100.0/bin/tmhmm/2.0c

interproscan-5.68-100.0/bin/tmhmm/2.0c$ ls

decodeanhmm.Linux_i386 decodeanhmm.Linux_ia64 TMHMM2.0.model tmhmm.ORIG decodeanhmm.Linux_i486 decodeanhmm.Linux_x86_64 TMHMM2.0.options decodeanhmm.Linux_i586 tmhmm tmhmmformat.pl decodeanhmm.Linux_i686 TMHMM1.0.model tmhmm_install.txt

interproscan.properties:

Binary file locations (required for setup.py)

binary.hmmer3.path=${bin.directory}/hmmer/hmmer3/3.3 phobius.signature.library.release=1.01 binary.phobius.pl.path=bin/phobius/1.01/phobius.pl

signalp_euk.signature.library.release=4.1 signalp_gram_positive.signature.library.release=4.1 signalp_gram_negative.signature.library.release=4.1 binary.signalp.path=bin/signalp/4.1/signalp signalp.perl.library.dir=bin/signalp/4.1/lib

tmhmm.signature.library.release=2.0c binary.tmhmm.path=bin/tmhmm/2.0c/decodeanhmm

tmhmm.model.path=data/tmhmm/2.0c/TMHMM2.0c.model

is it correct?

tgrego commented 2 months ago

No, there are some mixups in the files...

For tmhmm, all files are currently in bin/tmhmm/2.0c the file bin/tmhmm/2.0c/TMHMM2.0.model needs to be in data/tmhmm/2.0c/TMHMM2.0.model mv bin/tmhmm/2.0c/TMHMM2.0.model data/tmhmm/2.0c/TMHMM2.0.model Also the binary to be used is bin/tmhmm/2.0c/decodeanhmm, which does not exist. You'll need to rename the appropriate one for your system (usually Linux_x86_64) to the correct name cp bin/tmhmm/2.0c/decodeanhmm.Linux_x86_64 bin/tmhmm/2.0c/decodeanhmm That should be all to activate tmhmm.

For signalp, the files should be directly under bin/signalp/4.1/ (not bin/signalp/4.1/signalp). there should be a bin/signalp/4.1/signalp file (the binary) and also a bin/signalp/4.1/lib/ (that should contain a FASTA.pm file).

For phobius the required binaries need to be in bin/phobius/1.01/ so that actually seems correct

Paolopab commented 2 months ago

It seems that I installed SignalP 6, while InterProScan was looking for SignalP 4.1.

Once SignalP 4.1 was installed, I ran this command: ./interproscan.sh -i test_all_appl.fasta -f tsv -dp I got this error: - Command line failed with exit code: 2 Command: perl bin/signalp/4.1/signalp -T Error on binary output: Can't locate FASTA.pm in @INC (may need to install FASTA module). I did: nano bin/signalp/4.1/signalp use strict; use lib 'bin/signalp/4.1/lib'; After this, chmod +x bin/signalp/4.1/signalp ./interproscan.sh -i test_all_appl.fasta -f tsv -dp output:

nano bin/signalp/4.1/signalp. my $nnhowplayer = 'bin/signalp/4.1/bin/nnhowplayer.Linux_x86_64'; chmod +x bin/signalp/4.1/bin/nnhowplayer.Linux_x86_64

(base) user@user:~/interproscan-5.68-100.0$ ./interproscan.sh -i test_all_appl.fasta -f tsv -dp 17/06/2024 16:09:10:414 Benvenuti in InterProScan-5.68-100.0 17/06/2024 16:09:10:415 Esecuzione di InterProScan v5 in modalità STANDALONE... su Linux 17/06/2024 16:09:12:986 RunID: user_20240617_160912909_i41h 17/06/2024 16:09:18:401 Loading file /home/user/interproscan-5.68-100.0/test_all_appl.fasta 17/06/2024 16:09:18:402 Running the following analyses: [AntiFam-7.0,CDD-3.20,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2023_05,MobiDBLite-2.0,NCBIfam-14.0,PANTHER-18.0,Pfam-37.0,Phobius-1.01,PIRSF-3.10,PIRSR-2023_05,PRINTS-42.0,ProSitePatterns-2023_05,ProSiteProfiles-2023_05,SFLD-4,SignalP_EUK-4.1,SignalP_GRAM_NEGATIVE-4.1,SignalP_GRAM_POSITIVE-4.1,SMART-9.0,SUPERFAMILY-1.75,TMHMM-2.0c] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 17/06/2024 16:25:34:509 26% completed 17/06/2024 16:25:48:880 51% completed 17/06/2024 16:26:04:814 77% completed 17/06/2024 16:26:12:499 91% completed 17/06/2024 16:26:34:686 100% done: InterProScan analyses completed

Now, if I use the following command: interproscan.sh -i /home/user/file.faa -f tsv,gff3 -goterms -d /home/results/ -pa -cpu 28 -t p The output is: 2024-06-17 16:28:57,977 [amqEmbeddedWorkerJmsContainer-20] [uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener:216] ERROR - Execution thrown when attempting to executeInTransaction the StepExecution. All database activity rolled back. java.lang.IllegalStateException: Command line failed with exit code: 1 Command: bin/hmmer/hmmer3/3.3/hmmsearch -Z 65245 -E 0.001 --cpu 1 -o /home/user/interproscan-5.68-100.0/temp/user_20240617_162843616_9eqv//jobFunFam/000000004001_000000005357.raw.out data/gene3d/4.3.0/gene3d_main.hmm /home/user/interproscan-5.68-100.0/temp/user_20240617_162843616_9eqv//jobFunFam/000000004001_000000005357.fasta Error output from binary:

Error: File format problem in trying to open HMM file data/gene3d/4.3.0/gene3d_main.hmm. Opened data/gene3d/4.3.0/gene3d_main.hmm.h3m, a pressed HMM file; but format of its .h3i file unrecognized

Thank you so much for the support!!

tgrego commented 2 months ago

great, looks like you got signalp to work. Indeed it needs to be version 4.1

The error you're getting regarding gene3d indicates that something went wrong pressing the hmm files. You can repress them by running in the interproscan install dir: python3 setup.py -f interproscan.properties

Paolopab commented 2 months ago

It didn't work, but rm data/gene3d/4.3.0/gene3d_main.hmm.h3* bin/hmmer/hmmer3/3.3/hmmpress data/gene3d/4.3.0/gene3d_main.hmm nano interproscan.properties gene3d.hmm.library.path=data/gene3d/4.3.0/gene3d_main.hmm It works Thank you very much for your helpfulness and kindness! I wish you the best :)