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GATB / DiscoSnp

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
https://gatb.inria.fr/software/discosnp/
GNU Affero General Public License v3.0
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error: there was a problem with readFileName Dumping #36

Closed clorenzo1 closed 1 year ago

clorenzo1 commented 1 year ago

Hi Pierre,

I am reopening this issue as it was not resolved.

Thank you for the suggestion, although both methods (what I initially ran and what you suggested) for me produce the same file where each line has the full path and the file name as such:

/my/current/path/file1.fasta /my/current/path/file2.fasta

And I am still getting this error:

path/to/run_discoSnpRad.sh: line 553: /my/current/path../bin/read_file_names: No such file or directory "there was a problem with readFileName Dumping"

I also tried putting the script in the directory with the files and just having a list of files without the full paths. This produced the same error.

I also tried running the simple_test.sh script and got the following error:

"there was a problem with graph construction$ reset diff: discoRes_k_31_c_3_D_100_P_3_b_0_coherent.fa: No such file or directory *** Test: FAILURE on diff .fa"

Best! Coral

clorenzo1 commented 1 year ago

Hi there,

Apologies, I did not install the software correctly it seems and there were dependencies missing. It is now resolved and I will close the issue.

pierrepeterlongo commented 1 year ago

Great, thanks for these feed back.