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nataliedawson / code_to_check

Contains code for members of the group to check.
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Error: "couldn't open data/115699.ssap for reading" #2

Closed sillitoe closed 9 years ago

sillitoe commented 9 years ago

Reporting an error that I got when running this script with the test data:

perl get_rep_for_all_families.pl -i data/115699.faa -o data/ -d data/ -v 4.0
[2752] Processing functional family (115699) belonging to superfamily: data
[2752]  Opened FASTA file: data/115699.faa
[2752]  Cannot create folder ., it already exists...
[2752]  Cannot create folder for data, it already exists...
[2752]  Found 22 CATH structural domains
[2752]  Found 13 MD5 sequences
[2752]  At least two CATH structural domains found. Using SSAP method...
[2752]  Changing directory to data
[2752]  Checking SSAP matrix for completeness of file data/115699.ssap...
2015/01/06 11:56:34   INFO |    ...found 231 unique pairs
[2752]  231 SSAPs in original. Should be 231.
[2752] Writing SSAP file: data/115699.ssap
couldn't open data/115699.ssap for reading at get_rep_for_all_families.pl line 302.

Haven't looked into why this might be happening yet - might well be file permissions on my local setup or a problem in Cath::SsapList, but wanted to raise this issue as an example.

sillitoe commented 9 years ago

Ah, I've improved the error message in my local copy of Cath::SsapList - this now looks like:

couldn't open data/115699.ssap for writing: No such file or directory at get_rep_for_all_families.pl line 302.

Which is more useful. The problem seems to be down to changing directory, then using relative directory paths:

[4064]  Changing directory to data
...
[4064] Writing SSAP file: data/115699.ssap