TargetP returns all zeroes
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Entering edit mode
5.6 years ago
gdeiu89 • 0

Hello everyone, I am running TargetP on a set of protein sequences. I am running on a linux cloud computing system. After running it returns a "successfully completed" to me in stdout but reports all zeroes for every single protein sequence given.

targetp v1.1 prediction results

Number of query sequences: 999998 Cleavage site predictions included. Using NON-PLANT networks.

Name Len mTP SP other Loc RC TPlen

comp1_c0_seq1_2 63 0.000 0.000 0.000 ? 5 - comp1_c0_seq1_3 14 0.000 0.000 0.000 ? 5 - comp1_c0_seq1_4 31 0.000 0.000 0.000 ? 5 - comp1_c0_seq1_5 58 0.000 0.000 0.000 ? 5 - comp4_c0_seq1_1 48 0.000 0.000 0.000 ? 5 - comp4_c0_seq1_2 24 0.000 0.000 0.000 ? 5 - comp9_c0_seq1_1 22 0.000 0.000 0.000 ? 5 - comp9_c0_seq1_2 19 0.000 0.000 0.000 ? 5 - comp9_c0_seq1_3 14 0.000 0.000 0.000 ? 5 - comp9_c0_seq1_4 11 0.000 0.000 0.000 ? 5 - comp9_c0_seq1_5 29 0.000 0.000 0.000 ? 5 -

There are numerous sequences of over 1000 AAs and they also return zeroes.

I am running:

targetp -N -c ORF_1.fasta

Any ideas or suggestions?

Thanks, Greg

software error • 2.5k views
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Entering edit mode
5.3 years ago

TargetP does this when the query is too large. There may be other problems with your configuration, but 999,998 sequences is definitely too large of a query set. Try it with smaller subsets, like 100 or so to start.

I just wrote a python wrapper to help with this issue. Maybe it will be useful to you. https://breathmintsforpenguins.blogspot.com/2017/08/targetp-wrapper-for-large-queries.html

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