TargetP returns all zeroes

Question

[gdeiu89]

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

Answer 1

[Sean R Johnson]

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