Hello, On 2020-11-01 18:59, shruti gupta wrote: > shruti@debian:~/LoRTIA$ LoRTIA -5 AGAGTACATGGG --five_score 16 > --check_in_soft 15 -3 AAAAAAAAAAAAAAA --three_score 18 -s poisson -f > True ./test/test.sam ./output/ ./test/test_reads.fasta > Sorting ./test/test.sam... > Iterating over ./test/test.sam... > Generating statistics... > Sorting and indexing output... > Counting coverage... > Processed files saved to ./output/ > > Calculating l3 feature statistics... > Calculating r3 feature statistics... > Calculating r5 feature statistics... > Feature file ./output//test_r5.tsv is empty. There is nothing to do here. > Calculating l5 feature statistics... > Feature file ./output//test_l5.tsv is empty. There is nothing to do here. > Calculating in feature statistics... > ERROR: The specified reference file does not contain contigs > from the references used for mapping. Supply the same reference > that was used for the mapping and try again.
Looks like LoRTIA encountered an error. Is this a sample input coming from the LoRTIA upstream package? I would expect it to pass without errors, but maybe the upstream has added this test to demonstrate the limitations. Anyway I would suggest examining the situation before moving with the further packaging of LoRTIA. Best, Andrius
