Bam-readcount running for an extremely long time

[lukaas33]

I am running bam-readcount as part of an analysis of three samples. The first two finished in a few hours but the third has been running for 40h (with 100% use of one CPU) already.

/usr/bin/bam-readcount -f /shared_dir/reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa -l /tmp/tmp0jvVWr -w 0 -b 20 -q 0 /shared_dir/rna_expression.bam

I am running this via https://github.com/genome/docker-bam_readcount_helper-cwl which creates the regions from a vcf file. There is not something else in this script which is halting things, the command bam-readcount itself has been running for 40h.
I will attach the regions created by this script (for part after -l).

The reference is taken from ftp://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/

The RNA alignment was done using Hisat2.
I will attach the alignment.

https://tuenl-my.sharepoint.com/:u:/g/personal/l_c_a_w_v_osenbruggen_student_tue_nl/EeyC8Ig8s_FPlUmaHwYDv5QB9KfvgUs7r_fjsw4nzXBIBw?e=3Uds4R

[lukaas33]

Update, it finished running after 50h