Hi Everyone
With your support I am able to install and run the LoRTIA package
I have run one test file which is generating this output
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.
Could you all please suggest what I have to do next in this package.
Regards
Shruti Gupta