CristinaMoraru
commented
10 months ago There seems to be an error in Branch C, when runnign step 1C. Could you please check the error and log files found directly in the the project folder (/virclust/virclust_scripts/out). They are labeled with the step name: "step1C_std_err.txt" and "step1C_std_out.txt". Furthermore, in the folder 03C/ there should be more error and log files from the tools used during 1C. If you upload them here, I could check them and figure out what the problem is.
Hey!
I am trying to run VirClust standalone, but I am getting the following error message:
VirClust called with projdir=/virclust/virclust_scripts/out infile=/virclust/virclust_scripts/in/test.fasta step2C_Plot=T [1] "projdir=/virclust/virclust_scripts/out" [2] "infile=/virclust/virclust_scripts/in/test.fasta" [3] "step2C_Plot=T" [4] "sing=yes" [1] "Starting VirClust." [1] "Running VirClust step 0: writing one viral genome per fasta file." [1] "Step 2C was automatically activated (if you have not done so yourself), because it is required by other selected steps." [1] "Step 1C was automatically activated (if you have not done so yourself), because it is required by other selected steps." [1] "Step 1B was automatically activated (if you have not done so yourself), because it is required by other selected steps." [1] "Step 2A was automatically activated (if you have not done so yourself), because it is required by other selected steps." [1] "Step 1A was automatically activated (if you have not done so yourself), because it is required by other selected steps." [1] "Running VirClust step 1A: predict ORFs and translate to proteins." [1] "Step 1A has finished successfully with status 0." [1] "Running VirClust step 2A: clustering proteins based on BLASTp." [1] "Step 2A has finished successfully with status 0." [1] "Running VirClust step 1B: calculate protein superclusters based on HMMs" [1] "Step 1B has finished successfully with status 0." [1] "Running VirClust step 1C: calculate protein super-superclusters based on HMMs" [1] "Step 1C has finished with status 1, which represents an error. Aborting Virclust. Check the log files." Warning message: In dir.create(projdir) : '/virclust/virclust_scripts/out' already exists
Any help would be highly appreciated!
Thank you!