AlfredoKCL
commented
2 years ago Hello, we are in the process of updating DNAscan. I think it is best if you try the new version directly https://github.com/hevmarriott/DNAscanv2 . Let me know if you prefer to receive support for the older version instead BW Alfredo
Hi,
I am trying to use DNAscan, I do not have access to run sudo commands but I was able to accomplish do everything in these commands without access for sudo (except for tff-dejavu).
I am getting the folowing error:All_data/ALS57_CKDN200006030-1A_HLTMNDSXY_L3_filtered_snps.vcf | bgzip -c > All_data/DNAscan/SETUP/DNAscanOutput_snps/ALS57_CKDN200006030-1A_HLTMNDSXY_L3/sample_sorted_filtered.vcf.gz ; tabix -fp vcf All_data/DNAscan/SETUP/DNAscanOutput_snps/ALS57_CKDN200006030-1A_HLTMNDSXY_L3/sample_sorted_filtered.vcf.gz
WARNING: All_data/DNAscan/SETUP/DNAscanOutput_snps/ALS57_CKDN200006030-1A_HLTMNDSXY_L3/sample_sorted_filtered.vcf.gz only contains the header and no data, therefore DNAscan will now terminate."
"WARNING: Fastq format input data is required if you want to perform the alignment stage WARNING: Using input vcf as variant file. Do not provide vcf file if you wish to perform variant calling Hard filtering of SNV/indel variants is being performed... bcftools filter -i " QUAL > 1 & QUAL / INFO/AO > 10 & SAF > 0 & SAR > 0 & RPR > 1 & RPL > 1 "
The commands I used to call are: "DNAscan.py -in $VCF/${names[${SLURM_ARRAY_TASK_ID}]}_filtered_InDel.vcf -format vcf -reference hg38 -alsgenescanner -out $OUT DNAscan.py -in $VCF/${names[${SLURM_ARRAY_TASK_ID}]}_filtered_snps.vcf -format vcf -reference hg38 -alsgenescanner -out $OUT2"
I set up Annovar and all other dependecies to my knowledge. Do you have any troubleshooting suggestions? Also, I checked the path to the vcfs and it is correct, the vcf is not empty, but the file that gets copied into the output folder is.