Assertion error when running majiq build

[Athmaja Viswanath]

Hi, 

I am using nematode samples (Caenorhabditis remanei) for which I got the gff3 file from wormbase parasite (https://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/releases/WBPS16/species/caenorhabditis_remanei/PRJNA577507/caenorhabditis_remanei.PRJNA577507.WBPS16.annotations.gff3.gz)

 I used the same gff3 file to align the reads using STAR. when I run majiq build command I get something called an assertion error along with Warning-incorrect gff for some genes. I went and checked the gff3 file and for the genes that have warning there is no mrna/transcript information and so the warning make sense. However, it then gives me a second final error (i.e. assertion error) after which it stops running.

Code used for running majiq build 

majiq build caenorhabditis_remanei.PRJNA577507.WBPS16.annotations.gff3 -c vx3_cre.ini -o majiq_build_vx3_cre --disable-denovo-ir

I have attached screenshots of my gff3 file, the warnings and the assertion errors. Please let me know how I can proceed from here and if you need any other detail from me.  Your help is greatly appreciated!

Thanks a lot,

Athmaja

[San Jewell]

Hello,

It seems this gff3 file does not follow the standards format. Similar to TSV, there should be the same number of columns on every row. On a cursory look, it seems that on about line ~63349 there is a line missing a column (at well as many after it) , that is, there only seem to be 7 tab characters instead of eight. I believe this is the source of the assertion error.

As for the mRNA transcript warning, this may happen with some transcripts in the gff3 file used, but majiq should still run okay even if there are problems with some rows.

Let me know if it helps. I'd recommend reaching out to wormbase or writing a simple script to correct the problems.