checkchrom doesn't seem to work for me

[ls233]

My GTF have chromosomes names like GL00000*.* here is cmd I use: $ python /path/to/leafcutter/clustering/leafcutter_cluster_regtools.py
-j path/to/Aligned.sortedByCoord.out.bam.junc
-m 50 -o
-l 500000
--nochromcheck=checkchrom

Even though I include the option --nochromcheck=checkchrom , the tool still produces an error.

GL000009.2 55964 56572 JUNC00526257 2 - 55964 56572 255,0,0 2 120,94 0,514 does not exist... check your junction files.

[jackhump]

You're providing a single junction file as the -j argument.

It should instead be a file containing a list of paths to junction files.