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POSSUM not working due to incompatible pssm file

I generated a pssm file from psi-blast and then I am using POSSUM to generate a pse-pssm file to run a programme, ASPIRER, for identifying unconventionally secerted proteins. However I am running into issues with it the code I used to generate the pssm file is as follows:

psiblast \
  -db nr \
  -query /nesi/project/vuw03925/software/POSSUM_Standalone_Toolkit/input/test_lottia.fasta \
  -num_iterations 3 \
  -out_ascii_pssm /nesi/project/vuw03925/software/POSSUM_Standalone_Toolkit/output/test_lottia

This gave an out file, which i renamed to be a pssm file.

This was then run through POSSUM:

perl possum_standalone.pl \
  -i /scale_wlg_persistent/filesets/project/vuw03925/software/POSSUM_Standalone_Toolkit/input/test_lottia.fasta \
  -o /scale_wlg_persistent/filesets/project/vuw03925/software/POSSUM_Standalone_Toolkit/output/test_lottia_pse_pssm.csv \
  -t pse_pssm -p /scale_wlg_persistent/filesets/project/vuw03925/software/POSSUM_Standalone_Toolkit/input/pssm_files/lottia \
  -h T \
  -a 1

This was run successfully according to the job and error messages but I have no output file.

What am I doing wrong ?

Thanks for your help!

fasta pse-pssm pssm possum
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written by rianna.collins • rianna.collins

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
code_formatting

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written by Ram Ram

Thank you so much. I'm new to this and didn't realise there was a code option.

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written by rianna.collins • rianna.collins

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