Error: Don't know what format is!

[YichaoOU]

Hello,

Any clue what is wrong? I'm running the test data.

Thanks, Yichao

[yli11@noderome134 test_data]$ perl ../src/ESPRESSO_S.pl -A test_data_espresso_sirv/SIRV_C.gtf -L samples.tsv -F test_data_espresso_sirv/SIRV2.fasta -O test_result
 Work directory test_result does not exist. Make it by myself
 in samples.tsv does not exist or is not readable!
Don't know what format  is!
Perl exited with active threads:
    5 running and unjoined
    0 finished and unjoined
    0 running and detached

[EricKutschera]

Here is the line for that error message: https://github.com/Xinglab/espresso/blob/v1.3.0-beta/src/ESPRESSO_S.pl#L169

It's expecting samples.tsv to be a tab separated file where the first column in each line is a .sam or .bam file

The error message in your post has an empty space where the file path should be:

{file_path} in samples.tsv does not exist or is not readable!
Don't know what format {file_path} is!

I was able to reproduce that error message by adding a blank line at the end of my samples.tsv. Does your samples.tsv have a blank line?

[YichaoOU]

Yep, thanks!