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
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Is that your command verbatim?
If so, you have a space between
pythonand3which should not exist (not that I think this is the root of your error, but we need to be precise).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!
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/
$PATHissue, but need to be sure.