The bad parameters in targetp

[NailouZhang]

the pipline show

Caused by: Process targetP (1) terminated with an error exit status (2)

Command executed:

targetp -P -c input.1 > out_targetp_input.1

Command exit status: 2

Command output: (empty)

Command error: flag provided but not defined: -P Usage of targetp: -batch int Number of sequences that the tool will run simultaneously. Decrease or increase size depending on your system memory. (default 100) -fasta string Input file in fasta format. -format string Output format. 'long' for generating the predictions with plots, 'short' for the predictions without plots. (default "short") -gff3 Make gff3 file of processed sequences. -mature Make fasta file with mature sequence. -org string Organism. Non-plant: 'non-pl', Plant: 'pl' (default "non-pl") -plot string Plots output format. When long output selected, choose between 'png', 'eps' or 'none' to get just a tabular file. (default "png") -prefix string Output files prefix. (default "Input file prefix") -stdout Write the prediction summary to the STDOUT. -tmp string Specify temporary file directory. (default "System default tmpdir") -verbose Verbose output. Specify '-verbose=false' to avoid printing. (default true) -version Prints version.

In main.nf

process 'targetP' {

label 'sigtarp'

input:
file seq from seq_file2

output:
file("out_targetp_${seq}") into (targetP_result1, targetP_result2)

"""
targetp -P -c  $seq > out_targetp_${seq}
"""

So, how can I solve it?

[toniher]

Dear Nailou,

thanks for reporting! Can you point which targetP version are you using?

Thanks!

[NailouZhang]

Hi, Toniher I uesed targetp-2.0.Linux.tar.gz

[toniher]

Hi Nailou, pipeline is set up to work with targetP 1.1 version. More details here: https://github.com/biocorecrg/sigtarp_docker/tree/4f9a243a8491cac24dae78496990b4fa1b0a8b7b

We will try to provide a new pipeline release with updated software versions in the upcoming weeks. Hope it helps!

[NailouZhang]

Thank you very much. I'm sorry that I made a mistake here and did not check the version of this package.

[lyn320]

hi, I ran the local version of targetp-2.0.Linux.tar.gz (Default parameters) and the slurm files report:

TargetP-2.0 Organism: Non-Plant Timestamp: 20220309220806

ID Prediction noTP SP mTP CS Position

TRINITY_DN100003_c0_g1_i1.p3 noTP 0.958083 0.001913 0.040004
TRINITY_DN100008_c0_g1_i1.p1 noTP 0.605158 0.013404 0.381438
TRINITY_DN100089_c0_g1_i1.p1 noTP 0.999502 0.000194 0.000304 im confused about the 'noTP',can you tell me what does that mean and what can be my Filter criteria(SP or SP plus noTP) if im looking for sequence targeting extracellular. thank you so much!

[toniher]

Hi, your question is unrelated to this issue (that is already closed). On the other hand, that is a TargetP-specific question, instead of a FA-nf. In any case, you can check about it in the article of the program: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769257/

[lyn320]

Hi, your question is unrelated to this issue (that is already closed). On the other hand, that is a TargetP-specific question, instead of a FA-nf. In any case, you can check about it in the article of the program: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769257/

Oops... by the way, thank you so much for this reply!