I am trying to crop an alignment using CIAlign v1.1.0, but only get a log file as output, not an alignment file.
This is my command:
CIAlign --infile input.fasta --get_section --section_start 373 --section_end 1259 --keep_gaponly --outfile_stem outfile
The log file looks normal (no errors), the last two lines are:
2023-06-01 15:23:59,738 - __main__ - INFO - Nucleotide alignment detected2023-06-01 15:23:59,775 - __main__ - INFO - Cropping alignment to keep columns 373 to 1259
I tried the same using an .ini file instead of using arguments, but this gave the same result (a log file only, no alignment file).
Hi,
I am trying to crop an alignment using CIAlign v1.1.0, but only get a log file as output, not an alignment file.
This is my command:
CIAlign --infile input.fasta --get_section --section_start 373 --section_end 1259 --keep_gaponly --outfile_stem outfileThe log file looks normal (no errors), the last two lines are:
2023-06-01 15:23:59,738 - __main__ - INFO - Nucleotide alignment detected2023-06-01 15:23:59,775 - __main__ - INFO - Cropping alignment to keep columns 373 to 1259I tried the same using an .ini file instead of using arguments, but this gave the same result (a log file only, no alignment file).
Thank you for looking into this! Annelies