+ ACC=AF086833
+ SRR=SRR1972739
+ BAM=SRR1972739.bam
+ ALL=SRR1972739.all.vcf
+ VCF=SRR1972739.variants.vcf
+ REF=refs/AF086833.fa
+ GFF=refs/AF086833.gff
+ mkdir -p refs
+ bio fetch -format fasta AF086833
+ bio fetch -format gff AF086833
+ bwa index refs/AF086833.fa
[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 0.01 seconds elapse.
[bwa_index] Update BWT... 0.00 sec
[bwa_index] Pack forward-only FASTA... 0.00 sec
[bwa_index] Construct SA from BWT and Occ... 0.01 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index refs/AF086833.fa
[main] Real time: 0.407 sec; CPU: 0.012 sec
+ samtools faidx refs/AF086833.fa
+ mkdir -p reads
+ fastq-dump -X 10000 --split-files -O reads SRR1972739
+ R1=reads/SRR1972739_1.fastq
+ R2=reads/SRR1972739_2.fastq
+ bwa mem refs/AF086833.fa reads/SRR1972739_1.fastq reads/SRR1972739_2.fastq
+ samtools sort
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 20000 sequences (2020000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (738, 5739, 6, 663)
[M::mem_pestat] analyzing insert size distribution for orientation FF...
[M::mem_pestat] (25, 50, 75) percentile: (74, 114, 180)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 392)
[M::mem_pestat] mean and std.dev: (131.35, 75.24)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 498)
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (174, 220, 276)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 480)
[M::mem_pestat] mean and std.dev: (227.70, 77.37)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 582)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation RR...
[M::mem_pestat] (25, 50, 75) percentile: (77, 122, 175)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 371)
[M::mem_pestat] mean and std.dev: (131.18, 71.99)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 469)
[M::mem_process_seqs] Processed 20000 reads in 0.960 CPU sec, 0.958 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa reads/SRR1972739_1.fastq reads/SRR1972739_2.fastq
[main] Real time: 0.982 sec; CPU: 0.972 sec
+ samtools index SRR1972739.bam
+ bcftools mpileup -O v -f refs/AF086833.fa SRR1972739.bam
[mpileup] 1 samples in 1 input files
+ cat SRR1972739.all.vcf
+ bcftools call --ploidy 1 -mv -O v -o SRR1972739.variants.vcf