+ ACC=AF086833
+ REF=refs/AF086833.fa
+ GENOME=genome.fa
+ N=1000
+ BAM=results.bam
+ mkdir -p refs
+ rm -f log.txt
+ '[' '!' -f refs/AF086833.fa ']'
+ efetch -db nuccore -format fasta -id AF086833
+ bwa index refs/AF086833.fa
+ samtools faidx refs/AF086833.fa
+ '[' '!' -f genome.fa ']'
+ cp refs/AF086833.fa genome.fa
+ R1=read1.fq
+ R2=read2.fq
+ wgsim -N 1000 -e 0 -r 0 -R 0 genome.fa read1.fq read2.fq
[wgsim] seed = 1604503693
[wgsim_core] calculating the total length of the reference sequence...
[wgsim_core] 1 sequences, total length: 18959
+ bwa mem refs/AF086833.fa read1.fq read2.fq
+ samtools sort
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2000 sequences (140000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1000, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (466, 502, 536)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (326, 676)
[M::mem_pestat] mean and std.dev: (500.12, 50.12)
[M::mem_pestat] low and high boundaries for proper pairs: (256, 746)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2000 reads in 0.024 CPU sec, 0.025 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem refs/AF086833.fa read1.fq read2.fq
[main] Real time: 0.027 sec; CPU: 0.024 sec
+ samtools index results.bam