Bioinformatics Recipe Cookbook
Run Parameters
Parameters used during the run:
  • Genome Accession Number: NZ_CP008918
  • SRA Run Number: SRR4124989
Output Messages
Messages printed to the standard output stream:
Read 1047822 spots for SRR4124989
Written 1047822 spots for SRR4124989
*** Sequence statistics
file                      format  type   num_seqs      sum_len  min_len  avg_len  max_len
reads/SRR4124989_1.fastq  FASTQ   DNA   1,047,822  105,830,022      101      101      101
reads/SRR4124989_2.fastq  FASTQ   DNA   1,047,822  105,830,022      101      101      101
*** 
Other Messages
Messages printed to the standard error stream:
+ ACC=NZ_CP008918
+ SRR=SRR4124989
+ mkdir -p ref
+ REF=ref/NZ_CP008918.fa
+ efetch -db nuccore -id NZ_CP008918 -format fasta
+ mkdir -p reads
+ fastq-dump --origfmt --split-files -O reads SRR4124989
+ echo '*** Sequence statistics'
+ seqkit stat reads/SRR4124989_1.fastq reads/SRR4124989_2.fastq
+ echo '*** '
+ CPUS=4
+ R1=reads/SRR4124989_1.fastq
+ R2=reads/SRR4124989_2.fastq
+ samtools sort -l 0 --threads 4
+ minimap2 -a -x sr -t 4 ref/NZ_CP008918.fa reads/SRR4124989_1.fastq reads/SRR4124989_2.fastq
+ bcftools mpileup -Ou -B --min-MQ 60 -f ref/NZ_CP008918.fa -
+ bcftools call -Ou -v -m -
+ bcftools norm -Ou -f ref/NZ_CP008918.fa -d all -
+ bcftools filter -Ov -e 'QUAL<40 || DP<10 || GT!="1/1"'
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid
[M::mm_idx_gen::0.048*1.00] collected minimizers
[M::mm_idx_gen::0.058*1.46] sorted minimizers
[M::main::0.058*1.46] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.058*1.46] mid_occ = 1000
[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.061*1.44] distinct minimizers: 372863 (99.45% are singletons); average occurrences: 1.017; average spacing: 5.993
[M::worker_pipeline::2.762*4.08] mapped 495050 sequences
[M::worker_pipeline::4.508*4.22] mapped 495050 sequences
[M::worker_pipeline::6.001*4.26] mapped 495050 sequences
[M::worker_pipeline::7.181*3.91] mapped 495050 sequences
[M::worker_pipeline::7.420*3.80] mapped 115444 sequences
[M::main] Version: 2.12-r827
[M::main] CMD: minimap2 -a -x sr -t 4 ref/NZ_CP008918.fa reads/SRR4124989_1.fastq reads/SRR4124989_2.fastq
[M::main] Real time: 7.424 sec; CPU: 28.164 sec
[bam_sort_core] merging from 0 files and 4 in-memory blocks...
[mpileup] 1 samples in 1 input files
Lines   total/split/realigned/skipped:	45273/0/336/0
+ bcftools stats variants.vcf
+ plot-vcfstats -P -p plots variants-stats.txt
Parsing bcftools stats output: variants-stats.txt
Plotting graphs: python plot.py

Powered by the release 1.5.9