error: there was a problem with readFileName Dumping

[clorenzo1]

Hi,

I am trying to call SNPS from raw fasta files in my directory using the following command:

/my/discoSnp/path/discoSnpRAD/run_discoSnpRad.sh -r my_fof.txt

where my_fof.txt contains a list of files that created using the following command:

ls -d $PWD/*.fasta > my_fof.txt

and contains all the fasta files in my current working directory with their full path.

I keep getting the error "there was a problem with readFileName Dumping"

Do you know why this is?

Thanks!

[pierrepeterlongo]

Hey Can you check the fof file ? On my computer : ls -d $PWD/*.fasta > my_fof.txt generates

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

A good way to do it could be

for id in *.fasta; do echo $PWD/$id; done > my_fof.txt

I hope this helps

[clorenzo1]

Hi Pierre,

Thank you for the suggestion, although both methods f(what I initially ran and what you suggested) or 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 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.

Best! Coral

[clorenzo1]

Hi Perre,

Also just in case, I have tried running the simple_test.sh script and it gave 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"