One or more of your executables were not found. Please check back.

[Johnny3333]

Hello I am trying to run zUMIs with a small set of test data (2 samples).
This is the command I used bash bash /home/disk/songzq/Multi-omics_data/zUMIs-main/zUMIs.sh -y zumis_0930.yaml
I git cloned zUMIs and are using my own dependencies.
Below is my yaml file.
"project: zumis_0930
sequence_files:
file1:
name: /home/disk/songzq/202408161650_22FFVYLT4-X101SC24054945-Z01_Result/Rawdata/W1_S1_L001_R1_001.fq.gz
base_definition:
- BC( 1-8,27-34,53-60)
- UMI(61-68)
file2:
name: /home/disk/songzq/202408161650_22FFVYLT4-X101SC24054945-Z01_Result/Rawdata/W1_S1_L001_R2_001.fq.gz
base_definition: cDNA(1-150)
reference:
STAR_index: /home/disk/songzq/reference/STAR_mm10_n
GTF_file: /home/disk/songzq/reference/Mus_musculus.GRCm38.99.gtf
additional_STAR_params: ''
additional_files: ~
out_dir: /home/disk/songzq/Mouse_bone/output_zumis/
num_threads: 6
mem_limit: 0
filter_cutoffs:
BC_filter:
num_bases: 1
phred: 20
UMI_filter:
num_bases: 1
phred: 20
barcodes:
barcode_num: null
barcode_file: null
barcode_sharing: ''
automatic: yes
BarcodeBinning: 1
nReadsperCell: 100
demultiplex: no
counting_opts:
introns: yes
downsampling: '0'
strand: 0
Ham_Dist: 0
write_ham: no
velocyto: no
primaryHit: yes
twoPass: yes
make_stats: yes
which_Stage: Filtering
Rscript_exec: /home/disk/songzq/.conda/envs/R/bin/Rscript
STAR_exec: /home/softwares/STAR-2.7.3a/bin/Linux_x86_64/STAR
pigz_exec: /usr/bin/pigz
samtools_exec: /home/anaconda3/bin/samtools"
Below is the terminal output after I ran this line of code.
` You provided these parameters:
YAML file: SS3_human_2samples_test.yaml
zUMIs directory:
STAR executable STAR
STAR
samtools executable samtools
samtools
pigz executable pigz
pigz
Rscript executable Rscript
/usr/local/bin/Rscript
RAM limit: 0
zUMIs version 2.9.7

Mon13 Sep 2024 21:05:41 BST
One or more of your executables were not found. Please check back`

I don't know how to solve it. Can you provide some suggestions? Thanks!!