HAPDeNovo python script step 3 errors

Question

[kittys]

Hello

I am trying to run step 3 of the HAPDeNovo script, with this as my command:

python3 HAPDeNovo_step3.py --child child_id --parent1 parent1_id --parent2 parent2_id --child_id child_id --parent1_id parent1_id --parent2_id parent2_id --child_bam child.bam --parent1_bam parent1.bam --parent2_bam parent2.bam --reference hg19.fa --chr_start 1 --chr_end 1 --child_sex female --out_dir .

When I try to run it, I get these errors:

line 31: run_denovo_step3_merge_1.sh: command not found

denovo_step3_parent1_id_1.sh: command not found

denovo_step3_parent2_id_1.sh: command not found

denovo_step3_child_id_1.sh: command not found

I have checked the sample IDs using the sample_ID.py script. Please could you advise if this is a problem with my files, with the software itself or how the software was installed? I am using an institutional computing set up so didn't build this myself.

Many thanks for your help, Kitty

[Joe]

Is that your command verbatim?

If so, you have a space between python and 3 which should not exist (not that I think this is the root of your error, but we need to be precise).

[kittys]

Good point, this was a mistake with me copying the command onto here, there isn't a space when running it so will edit this!

[Joe]

Can you provide a link to the source code for the script? The errors imply the python script calls a bunch of shell scripts which arent found. This is likely an install/$PATH issue, but need to be sure.