IndexError

[apritch]

Hi. I can see there is an open issue with the same error - did you get any further with this? I am getting the following error trying to run a 6mb adaptive nanopore sequencing run:

no reads aligned to chromosome chr1, skipping... no reads aligned to chromosome chr2, skipping... no reads aligned to chromosome chr3, skipping... no reads aligned to chromosome chr4, skipping... no reads aligned to chromosome chr5, skipping... no reads aligned to chromosome chr6, skipping... no reads aligned to chromosome chr7, skipping... no reads aligned to chromosome chr8, skipping... no reads aligned to chromosome chr9, skipping... no reads aligned to chromosome chr10, skipping... /opt/methphaser/./meth_phaser_parallel:235: FutureWarning: When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass (name,) instead of name to silence this warning. phased_df_chr.get_group(chromosome).iterrows() Traceback (most recent call last): File "/opt/methphaser/./meth_phaser_parallel", line 283, in main(sys.argv[1:]) File "/opt/methphaser/./meth_phaser_parallel", line 252, in main skipping_pair_start_list.append(phased_block_distance_list_sorted[0][0]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^ IndexError: list index out of range

The command used was: ./meth_phaser_parallel -b /data/t2t_whatshap_output/haplotagged.bam -r /data/reference_genomes/t2t/chm13v2.0.fa -g /data/t2t_whatshap_output/phased.gtf -vc /data/t2t_whatshap_output/phased.vcf.gz -o ./work

I have done the exact run - same steps - but aligned to hg38 with no issue. The hg38 has 2 phase blocks, this only has one. Any thoughts? Many thanks in advance.