minimap2 -a -x map-ont -t 16 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747_filtered.fastq.gz | samtools view -bS -F 4 - | samtools sort -o 817747.sorted.bam -	0.9315497740000183
samtools index 817747.sorted.bam	0.059654379999983576
align_trim  --normalise 500 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --start --remove-incorrect-pairs --report 817747.alignreport.txt < 817747.sorted.bam 2> 817747.alignreport.er | samtools sort -T 817747 - -o 817747.trimmed.rg.sorted.bam	1.1905963770000199
align_trim  --normalise 500 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --remove-incorrect-pairs --report 817747.alignreport.txt < 817747.sorted.bam 2> 817747.alignreport.er | samtools sort -T 817747 - -o 817747.primertrimmed.rg.sorted.bam	1.2235491870000033
samtools index 817747.trimmed.rg.sorted.bam	0.05301858899997569
samtools index 817747.primertrimmed.rg.sorted.bam	0.0537426509999932
medaka consensus --model r1041_e82_400bps_fast_g632 --threads 16 --chunk_len 800 --chunk_ovlp 400 --RG nCoV-2019_1 817747.trimmed.rg.sorted.bam 817747.nCoV-2019_1.hdf	6.52982628999996
medaka variant external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.nCoV-2019_1.hdf 817747.nCoV-2019_1.vcf	1.9771397060000027
medaka tools annotate --pad 25 --RG nCoV-2019_1 817747.nCoV-2019_1.vcf external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.trimmed.rg.sorted.bam 817747.medaka-annotate.vcf	1.8574154990000125
mv 817747.medaka-annotate.vcf 817747.nCoV-2019_1.vcf	0.00715678200003822
medaka consensus --model r1041_e82_400bps_fast_g632 --threads 16 --chunk_len 800 --chunk_ovlp 400 --RG nCoV-2019_2 817747.trimmed.rg.sorted.bam 817747.nCoV-2019_2.hdf	6.087260339999943
medaka variant external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.nCoV-2019_2.hdf 817747.nCoV-2019_2.vcf	1.9795514460000732
medaka tools annotate --pad 25 --RG nCoV-2019_2 817747.nCoV-2019_2.vcf external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.trimmed.rg.sorted.bam 817747.medaka-annotate.vcf	1.850302812000109
mv 817747.medaka-annotate.vcf 817747.nCoV-2019_2.vcf	0.0072282380000388
artic_vcf_merge 817747 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed 2> 817747.primersitereport.txt nCoV-2019_1:817747.nCoV-2019_1.vcf nCoV-2019_2:817747.nCoV-2019_2.vcf	0.44350526900007026
bgzip -f 817747.merged.vcf	0.009376342999985354
tabix -p vcf 817747.merged.vcf.gz	0.0074891279999746985
artic-tools check_vcf --summaryOut 817747.vcfreport.txt 817747.merged.vcf.gz external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed 2> 817747.vcfcheck.log	0.04274727400002121
artic_vcf_filter --medaka --min-depth 20 --min-qual 20 --nanopolish-qual-cov-ratio 3.0 817747.merged.vcf.gz 817747.pass.vcf 817747.fail.vcf	0.43024213400008193
artic_make_depth_mask --depth 20 external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.primertrimmed.rg.sorted.bam 817747.coverage_mask.txt	7.802679403999946
artic_mask external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta 817747.coverage_mask.txt 817747.fail.vcf 817747.preconsensus.fasta	0.5036027859999876
bcftools norm --check-ref x --fasta-ref 817747.preconsensus.fasta -O z -o 817747.pass.vcf.gz 817747.pass.vcf	0.030738146000089728
tabix -p vcf 817747.pass.vcf.gz	0.007691376999900967
bcftools consensus -f 817747.preconsensus.fasta 817747.pass.vcf.gz -m 817747.coverage_mask.txt -o 817747.consensus.fasta	0.044098138999970615
artic_fasta_header 817747.consensus.fasta "817747/ARTIC/medaka"	0.13843782399999327
cat 817747.consensus.fasta external_primer_schemes/nCoV-2019/V1200/nCoV-2019.reference.fasta > 817747.muscle.in.fasta	0.008325249999984408
muscle -in 817747.muscle.in.fasta -out 817747.muscle.out.fasta	13.84492464699997
artic_get_stats --min-depth 20 --scheme external_primer_schemes/nCoV-2019/V1200/nCoV-2019.scheme.bed --align-report 817747.alignreport.txt --vcf-report 817747.vcfreport.txt 817747	0.44607080499997664