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Issue with reference FASTA file in running ESPRESSO_S.pl #12

Closed jamesoccean closed 1 year ago

jamesoccean commented 1 year ago

Hello,

I am trying to run ESPRESSO_S.pl but running into an error with using the FASTA file that I used in the mapping stage. I keep receiving an error that reads, for instance,

Don't know what format AGGATGACATCACAGAGAACATTCAGGCCTCAAACCTAAATATTCAGATCTGAGGTTGGG is! CTTCCCCAGCCCCGCCCCCTCACTTCCGGTCGGACCGCACTGGGCAGAAGCCCGTG in genome.fa does not exist or is not readable! Don't know what format CTTCCCCAGCCCCGCCCCCTCACTTCCGGTCGGACCGCACTGGGCAGAAGCCCGTG is!

Should I make any adjustments to the FASTA file before running ESPRESSO_S.pl? I also tried using a transcripts FASTA file to no avail.

EricKutschera commented 1 year ago

It looks like this is the line that gives that error: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_S.pl#L169

That code is for parsing the sample file given on the commandline with -L (or --list_samples). Can you check the arguments in your command to see if genome.fa is used with -L (instead of -F)

jamesoccean commented 1 year ago

Thank you- it works! Error on my part.