Closed joshwkearney closed 3 years ago
The -d
flag will include everything in the directory. There appears to be a .DS_Store
file in your genomes
folder:
(base) bkille@tripp:~/temp$ ls -la genomes/
total 368
drwxr-xr-x 2 bkille bkille 4096 Jun 9 11:59 .
drwxrwxr-x 4 bkille bkille 4096 Jun 10 20:13 ..
-rw-r--r-- 1 bkille bkille 6148 Jun 9 11:59 .DS_Store
-rw-r--r-- 1 bkille bkille 30647 Jun 8 17:43 myseq10.fa
-rw-r--r-- 1 bkille bkille 30622 Jun 8 17:43 myseq11.fa
-rw-r--r-- 1 bkille bkille 30622 Jun 8 17:43 myseq1.fa
-rw-r--r-- 1 bkille bkille 30607 Jun 8 17:43 myseq2.fa
-rw-r--r-- 1 bkille bkille 30634 Jun 8 17:43 myseq3.fa
-rw-r--r-- 1 bkille bkille 30659 Jun 8 17:43 myseq4.fa
-rw-r--r-- 1 bkille bkille 30621 Jun 8 17:43 myseq5.fa
-rw-r--r-- 1 bkille bkille 30622 Jun 8 17:43 myseq6.fa
-rw-r--r-- 1 bkille bkille 30621 Jun 8 17:43 myseq7.fa
-rw-r--r-- 1 bkille bkille 30623 Jun 8 17:43 myseq8.fa
-rw-r--r-- 1 bkille bkille 30612 Jun 8 17:43 myseq9.fa
I'm running ParSNP v1.5.4 (installed from conda) and ran into a behavior that seems to be a regression from v1.2.
What's expected After running the command
parsnp -r ./covid.fa -d ./genomes/ -o ./results/
ParSNP should align the genomes in./genomes/
and output the results.What happens ParSNP fails with the output:
Workarounds This error can be avoided by using the command
parsnp -r ./covid.fa -d ./genomes/*.fa -o ./results/
, or by specifying each.fa
file individually as a list, or by using ParSNP v1.2 instead of 1.5.4.I'm unsure if specifying a directory for the
-d
option is supported in v1.5.4 because it isn't mentioned in the help menu, but it was supported in v1.2 and I would expect the two to be compatible. Not a big deal either way, but a more helpful error message would be appreciated. All my test data is attached in a zip. Thanks!data.zip