Unable to locate database file sampling/fragpicker_rama_tables/H_

Question

[ducfabulous]

Hi, I got this error when running fragment_picker from Rosetta 3:

    fragment_picker.linuxgccrelease @flags
    ....
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_T.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_T.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_T.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_A.counts
    basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
    .counts: [ WARNING ] Unable to locate database file sampling/fragpicker_rama_tables/H_
    .counts"xception Database file open failed for: "sampling/fragpicker_rama_tables/H_

It seems that the application trying to read the file "H_" but it doesn't exists. It's missing the final character of the file name and the .counts extension, should be H_x.counts instead. Anyone know why this issue happen and how to fix it ? Thank you all!

Answer 1

[ducfabulous]

Ok, i found the issue. It comes from the input .fasta file . I'm working on Windows and the notepad/notepad++ use both character CR+LF for line ending when I save the fasta file. Replace it with a single character LF - ( linux-compatible line ending) will solves this issue.