Question: interproscan empty output
0
gravatar for agata88
8 months ago by
agata88770
Poland
agata88770 wrote:

Hi all!

I have a problem with interproscan. After huge amount of hours it gave me an empty output. I am running it in the cloud - 32 CPU, 256G RAM. here is a command:

./interproscan.sh -i file.fasta -o file_interproscan_GO_KEGG.tsv -f tsv -dp --goterms --pathways --appl Pfam,SUPERFAMILY,SMART -cpu 32 > log_interproscan.txt 2>&1 &

No errors in log file:

29/07/2018 13:11:56:362 Welcome to InterProScan-5.30-69.0 29/07/2018 13:12:02:638 Running InterProScan v5 in STANDALONE mode... on Linux 29/07/2018 13:12:13:489 Loading file /home/bioidea/input/SuperDuper_orfs.fasta 29/07/2018 13:12:13:493 Running the following analyses: [Pfam-31.0,SMART-7.1,SUPERFAMILY-1.75] Pre-calculated match lookup service DISABLED. Please wait for match calculations to complete... 29/07/2018 13:12:17:589 Uploaded/Stored 16559 unique sequences for analysis 29/07/2018 14:06:51:528 25% completed 29/07/2018 14:49:48:346 50% completed 29/07/2018 15:49:48:396 70% completed 29/07/2018 16:49:48:400 70% completed 29/07/2018 17:49:48:453 70% completed 29/07/2018 18:49:48:470 70% completed 29/07/2018 19:49:48:537 70% completed 29/07/2018 20:49:48:659 70% completed 29/07/2018 21:49:48:750 70% completed 29/07/2018 22:49:48:868 70% completed 29/07/2018 23:49:48:917 70% completed 30/07/2018 00:49:48:920 70% completed 30/07/2018 01:49:48:926 70% completed 30/07/2018 02:49:48:969 70% completed 30/07/2018 03:49:49:079 70% completed 30/07/2018 04:49:49:151 70% completed 30/07/2018 05:49:49:191 70% completed 30/07/2018 06:49:49:199 70% completed 30/07/2018 07:49:49:215 86% completed 30/07/2018 08:49:49:329 95% completed 30/07/2018 09:49:49:390 95% completed 30/07/2018 10:49:49:503 95% completed 30/07/2018 11:40:53:944 100% done: InterProScan analyses completed

What is wrong here? The file_interprposcan_GO_KEGG.tsv is created but empty!

Thanks for any suggestions. PS. I am running interproscan-5.30-69.0.

interproscan • 320 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by agata88770

There is no info in the log file log_interproscan.txt ? Is there enough space on your machine ?

ADD REPLYlink written 8 months ago by Medhat8.2k

No error ...the log is above. 100% completed. I run it on 256GB of RAM and 1 TB of disc space so I don't think it's memory or disc.

ADD REPLYlink written 8 months ago by agata88770

Did you run the program with the test files as mentioned on https://github.com/ebi-pf-team/interproscan/wiki/HowToRun#interproscan-5-test-run? Did it run without any errors? Could you confirm whether you are providing protein or nucleotide sequences as input?

ADD REPLYlink written 8 months ago by Sej Modha4.1k

Yes, i Run test without error. Everything looked fine, that is why i 've decided to Run it on my protein sequences. The input includes orf aa sequences.

ADD REPLYlink modified 8 months ago • written 8 months ago by agata88770

Is it likely that no hits would be found for input amino acid sequences against the databases specified here, --appl parameter?

ADD REPLYlink written 8 months ago by Sej Modha4.1k

That would be a suprise for me. I dont think it is possible, i have blastx annotations for those sequences.

ADD REPLYlink written 8 months ago by agata88770

I'd extract that specific sequence where BLASTX hit was found and search that AA sequence against Pfam, SUPERFAMILY, SMART on InterPro. It is possible that domain signatures may not be found even though BLAST hits are found a sequence.

ADD REPLYlink written 8 months ago by Sej Modha4.1k
0
gravatar for agata88
8 months ago by
agata88770
Poland
agata88770 wrote:

So, I've made a mistake and gave as input orf nucleotide sequences. Program used it as amino acids sequences and gave empty output because of no hits found. The correct way is to include option -t n in command line above.

PS. I think, it might be helpful to have an error or even warning at the beginning of calculations when different than defauld input type is included. This will avoid similar problems in the future.

Best,

Agata

ADD COMMENTlink written 8 months ago by agata88770
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