search

vlothec / TRASH

RepeatIdentifier
MIT License
50 stars 3 forks source link

task1 error - cannot change working directory #2

Closed goertzenlr closed 1 year ago

goertzenlr commented 1 year ago

entire TRASH executable downloaded, (trash_install succeeds as test), new R in conda env. - test run on 30kb fasta:

[1] "Currently registered parallel backend name, version and cores" [1] "doParallelMC" [1] "1.0.17" [1] 1 [1] "Sequences to analyse:" file.name fasta.name 2 test.fa Contig1 [1] "2023-05-15 09:47:17 CDT" [1] "Working on sequence 1" [1] "Repeat Identification new" [1] "test_out1" [1] "test.fa" Error in { : task 1 failed - "cannot change working directory" Calls: %dopar% -> Execution halted

vlothec commented 1 year ago

Hi, can you provide the command you used? The only way I can replicate this error is when the output directory has a typo. The output directory also needs to be an absolute path, or no path at all (then output is placed where the command is run from).

goertzenlr commented 1 year ago

thanks, my error. I took the instructions to mean if no path info in front of the output directory name, it would be placed where command is run from.

./TRASH_run.sh test.fa

... ...

[1] "Currently registered parallel backend name, version and cores" [1] "doParallelMC" [1] "1.0.17" [1] 1 [1] "Sequences to analyse:" file.name fasta.name 2 test.fa Contig1 [1] "2023-05-16 08:32:02 CDT" [1] "Working on sequence 1" [1] "Repeat Identification new" [1] "/home/Documents/installs/TRASH" [1] "test.fa" [[1]] NULL

      used  (Mb) gc trigger  (Mb) max used  (Mb)

Ncells 2595200 138.6 4868417 260.1 4868417 260.1 Vcells 4447698 34.0 10146329 77.5 7160664 54.7 [1] "Finished working on sequence 1" [1] "2023-05-16 08:32:08 CDT" [1] "saving repeats" [1] "/home/Documents/installs/TRASH" character(0) Error in file(file, "rt") : cannot open the connection Calls: read.csv -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file 'NA': No such file or directory Execution halted

vlothec commented 1 year ago

Yes, the run goes through almost to the end. It seems like there are no repeats identified within the test.fa sequence. Is it a particuarly short sequence? Maybe there is something else that would throw TRASH off. Seems like nothing is identified first and then crashes trying to plot it.

If you try to test TRASH using provided test sequence (example_run/CP068268_39050443_39150442.fa), you might see if the program works as intended for you.

goertzenlr commented 1 year ago

correct, 30 kb fragment used to test, likely no major repeats, thought it might have clean exit status. will test with more realistic scaffold. thanks