Hi, I encountered an error when running generate_introns.py:
(base) [xfu1@sjgenappprdn01 hg38]$ python2 /export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py --genome /export/home/xfu1/hg38/Homo_sapiens.GRCh38.dna.alt.fa --gtf /export/home/xfu1/hg38/Homo_sapiens.GRCh38.108.gtf --extend 20 --out /export/home/xfu1/Profiler/Profiler/kma/out_dir
INFO: Reading in GTF: /export/home/xfu1/hg38/Homo_sapiens.GRCh38.108.gtf
INFO: Grouping transcripts by gene
INFO: Writing intron BED file: /export/home/xfu1/Profiler/Profiler/kma/out_dir/introns.bed
INFO: Computing intron-to-transcript compatability
INFO: Opening FASTA: /export/home/xfu1/hg38/Homo_sapiens.GRCh38.dna.alt.fa
INFO: Note: will take a while the first time it is opened.
Traceback (most recent call last):
File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 154, in
main()
File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 151, in main
bed_to_introns(bed_out, args.genome, introns_out)
File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 55, in bed_to_introns
seq = fasta[ref][int(start):int(stop)]
File "/export/home/xfu1/.local/lib/python2.7/site-packages/pyfasta/fasta.py", line 128, in getitem
c = self.index[i]
KeyError: '11'
I used the human reference genome downloaded from ensembl. Can someone help me to fix it? Thanks in advance!
-Eddie
Hi, I encountered an error when running generate_introns.py:
(base) [xfu1@sjgenappprdn01 hg38]$ python2 /export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py --genome /export/home/xfu1/hg38/Homo_sapiens.GRCh38.dna.alt.fa --gtf /export/home/xfu1/hg38/Homo_sapiens.GRCh38.108.gtf --extend 20 --out /export/home/xfu1/Profiler/Profiler/kma/out_dir INFO: Reading in GTF: /export/home/xfu1/hg38/Homo_sapiens.GRCh38.108.gtf INFO: Grouping transcripts by gene INFO: Writing intron BED file: /export/home/xfu1/Profiler/Profiler/kma/out_dir/introns.bed INFO: Computing intron-to-transcript compatability INFO: Opening FASTA: /export/home/xfu1/hg38/Homo_sapiens.GRCh38.dna.alt.fa INFO: Note: will take a while the first time it is opened. Traceback (most recent call last): File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 154, in
main()
File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 151, in main
bed_to_introns(bed_out, args.genome, introns_out)
File "/export/home/xfu1/Profiler/Profiler/kma/inst/pre-process/generate_introns.py", line 55, in bed_to_introns
seq = fasta[ref][int(start):int(stop)]
File "/export/home/xfu1/.local/lib/python2.7/site-packages/pyfasta/fasta.py", line 128, in getitem
c = self.index[i]
KeyError: '11'
I used the human reference genome downloaded from ensembl. Can someone help me to fix it? Thanks in advance! -Eddie