Error 'KeyError:3'

[lynnyi]

Please see my error trying to preprocess using kma

lynnyi⟫ python2.7 /home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py --genome ~/genomes/Mus_musculus.GRCm38.dna.alt.fa --gtf ~/genomes/Mus_musculus.GRCm38.91.gtf --extend 20 --out ~/introns INFO: Reading in GTF: /home/lynnyi/genomes/Mus_musculus.GRCm38.91.gtf INFO: Grouping transcripts by gene INFO: Writing intron BED file: /home/lynnyi/introns/introns.bed INFO: Computing intron-to-transcript compatability INFO: Opening FASTA: /home/lynnyi/genomes/Mus_musculus.GRCm38.dna.alt.fa INFO: Note: will take a while the first time it is opened. Traceback (most recent call last): File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 154, in main() File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 151, in main bed_to_introns(bed_out, args.genome, introns_out) File "/home/lynnyi/R/x86_64-pc-linux-gnu-library/3.4/kma/pre-process/generate_introns.py", line 55, in bed_to_introns seq = fasta[ref][int(start):int(stop)] File "/usr/local/lib/python2.7/dist-packages/pyfasta/fasta.py", line 128, in getitem c = self.index[i] KeyError: '3'

[BioLaoXu]

I have the same problem，has anyone solved the problem yet?

[edwardfu11]

I have the same problem -- did this issue be resolved? Thanks for sharing the solution. Thanks! -Eddie