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sameerkhurana10 / DSOL_rv0.2

deep protein solubility prediction
MIT License
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cannot access '../SCRATCH-1D_1.1/tmp/.../dataset.pro' #9

Open MZX998 opened 7 months ago

MZX998 commented 7 months ago

Dear all, I followed all the installation instructions and I succesfully installed the program (and dependencies). but when I run the command:

R --vanilla < scripts/PaRSnIP.R data/Seq_solo.fasta <path-to-your-scratch-installation>/bin/run_SCRATCH-1D_predictors.sh new_test 32

(once specified the right directories) this error occurs:

###################################
#                                 #
#  SCRATCH-1D release 1.1 (2015)  #
#                                 #
###################################

[SCRATCH-1D_predictions.pl] 1 protein sequence(s) found
[SCRATCH-1D_predictions.pl] generating sequence profiles...
chmod: cannot access '/my/path/DSOL_rv0.2/SCRATCH-1D_1.1/tmp/20240126-161014-720423000963/dataset.pro': No such file or directory
[SCRATCH-1D_predictions.pl] failed generating sequence profiles...
[1] 1
Error in file(file, "r") : cannot open the connection
Calls: PaRSnIP ... PaRSnIP.calc.features.test -> as.vector -> read.fasta -> scan -> file
In addition: Warning message:
In file(file, "r") :
  cannot open file '/tmp/RtmpQlBOft/tmp560bd37c91444.ss': No such file or directory
Execution halted

Then I gave the permission to that folder, so i run again the command but the same error occurs in another tmp dir (every time is created a new dir in "tmp" dir. In addition, this error occurs by simply running the test in the README file provided in the SCRATCH-1D 1-1 folder.

Thank you for your attention Matteo

sezaz-acog commented 7 months ago

follow this closed issue to solve it.

https://github.com/sameerkhurana10/DSOL_rv0.2/issues/2 if this also doesent solve it. try converting all your aminoacid sequences from fasta into uppercase letters and see.