maiziex
commented
1 year ago Let me check with you for one thing first. Do you run steps 1 and step 2 for all chromosomes? or just run chr1 through "--chr_start 1 --chr_end 1 " at previous steps? Can you also check do you have "Aquila_Contig_chr*.fasta" for every chromosome in the "Assembly_Contigs_files" after you finished step2.
Assembly_Contigs_files (Aquila_step2) |-Aquila_Contig_chr*.fasta --> (final contigs for each chromosome) └-Aquila_contig.fasta
Hi I'm using aquila on my linked-reads data and it apparently works well with steps 1 and 2. If I well unstersttod, there are other 2 steps in order to performe assembly and phasing of the structural variants (Aquila_assembly_based_variants_call.py" and "Aquila_phasing_all_variants.py). I run the command without any kind of errors, but my final vcf (Aquila_final_sorted.vcf) contains only the chr1. These are the outputs but all except the chr1 file, are empty: Aquila_DEL_chr10.vcf Aquila_final.vcf Aquila_SNPs_chr10.vcf Aquila_DEL_chr11.vcf Aquila_INS_chr10.vcf Aquila_SNPs_chr11.vcf Aquila_DEL_chr12.vcf Aquila_INS_chr11.vcf Aquila_SNPs_chr12.vcf Aquila_DEL_chr13.vcf Aquila_INS_chr12.vcf Aquila_SNPs_chr13.vcf Aquila_DEL_chr14.vcf Aquila_INS_chr13.vcf Aquila_SNPs_chr14.vcf Aquila_DEL_chr15.vcf Aquila_INS_chr14.vcf Aquila_SNPs_chr15.vcf Aquila_DEL_chr16.vcf Aquila_INS_chr15.vcf Aquila_SNPs_chr16.vcf Aquila_DEL_chr17.vcf Aquila_INS_chr16.vcf Aquila_SNPs_chr17.vcf Aquila_DEL_chr18.vcf Aquila_INS_chr17.vcf Aquila_SNPs_chr18.vcf Aquila_DEL_chr19.vcf Aquila_INS_chr18.vcf Aquila_SNPs_chr19.vcf Aquila_DEL_chr1.vcf Aquila_INS_chr19.vcf Aquila_SNPs_chr1.vcf Aquila_DEL_chr20.vcf Aquila_INS_chr1.vcf Aquila_SNPs_chr20.vcf Aquila_DEL_chr21.vcf Aquila_INS_chr20.vcf Aquila_SNPs_chr21.vcf Aquila_DEL_chr22.vcf Aquila_INS_chr21.vcf Aquila_SNPs_chr22.vcf Aquila_DEL_chr23.vcf Aquila_INS_chr22.vcf Aquila_SNPs_chr23.vcf Aquila_DEL_chr2.vcf Aquila_INS_chr23.vcf Aquila_SNPs_chr2.vcf Aquila_DEL_chr3.vcf Aquila_INS_chr2.vcf Aquila_SNPs_chr3.vcf Aquila_DEL_chr4.vcf Aquila_INS_chr3.vcf Aquila_SNPs_chr4.vcf Aquila_DEL_chr5.vcf Aquila_INS_chr4.vcf Aquila_SNPs_chr5.vcf Aquila_DEL_chr6.vcf Aquila_INS_chr5.vcf Aquila_SNPs_chr6.vcf Aquila_DEL_chr7.vcf Aquila_INS_chr6.vcf Aquila_SNPs_chr7.vcf Aquila_DEL_chr8.vcf Aquila_INS_chr7.vcf Aquila_SNPs_chr8.vcf Aquila_DEL_chr9.vcf Aquila_INS_chr8.vcf Aquila_SNPs_chr9.vcf Aquila_DEL.vcf Aquila_INS_chr9.vcf Aquila_SNPs.vcf Aquila_final_sorted.vcf Aquila_INS.vcf
I tried with several sample but same results Can you help me, please?