Entering edit mode
20 days ago
rianna.collins
•
0
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!
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