GillyG

That is true. Solved now. Thanks a lot !

Thanks a lot! I got a new bed file and still get errors, I understand the last error about the not allowed characters but I don't understand the other ones...

Thanks, Now with 'normal' IDs it stills trows some of the warnings as before and it moves a bit forward but stalls later. ``` head /work/FAC/FBM/Drosophila_genome/dm6.refGene.gtf.bed chrX 11933704 11983915 NM_001370018...

But in theory that's not true because: 1. The bit file was build using the fasta file where the headers have the .1 ``` make_lastz_chains/HL_kent_binaries/faToTwoBit /work/FAC/FBM/Gilly/genome/mod_GCA_030586385.1_ASM3058638v1_genomic.fna mod_GCA_030586385.1_ASM3058638v1_genomic.2bit grep -e ">"...

Thanks! Yes, I got that. But in theory they all match since they all have the .1 (in both fasta and 2bit file). Which is why i dont understand the...

Thanks for the answer. I tried to install and run again just with the example and I get the same chain_run error: ``` ./make_chains.py target query test_data/test_reference.fa test_data/test_query.fa --pd test_out...