I have a question about the file.log when OMA start to convert the files.
I download 30 coding genomes of different species from Ensembl or NCBI. In order to eliminate the transcripts and isoforms I used cd-hitest first and then I passed the files through TRANSDECODER.
When I start running OMA in the .log file shows me many of these errors:
WARNING: IUPAC ambiguity characters for DNA/RNA not supported. Will replace them with 'X' Pre-processing input (DNA) 19099 sequences within 19099 entries considered Creating file Cache/DB/Balaena_mysticetus.db.map for mapping Building new Pat index in file Cache/DB/Balaena_mysticetus.db.tree with 27254391 entries Pat index with 27254391 entries sorted, from "A</SEQ></E>\n" to "XXXXXXXXXXXXXXXXXXX" Reading 44567976 characters from file Cache/DB/Balaenoptera_acutorostrata.db Pre-processing input (DNA) 20993 sequences within 20993 entries considered Creating file Cache/DB/Balaenoptera_acutorostrata.db.map for mapping Building new Pat index in file Cache/DB/Balaenoptera_acutorostrata.db.tree with 37893972 entries Pat index with 37893972 entries sorted, from "A</SEQ></E>\n" to "XXXXXXXXXXXXXXXXXXX"
I want to know if that errors can generate some problems with the normal run of OMA?