--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.log	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,261 @@
+### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b_out_dev --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
+
+### samtools faidx reference/ref.fa
+
+
+### bwa index reference/ref.fa
+
+[bwa_index] Pack FASTA... 0.00 sec
+[bwa_index] Construct BWT for the packed sequence...
+[bwa_index] 0.00 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... 0.00 sec
+[main] Version: 0.7.17-r1188
+[main] CMD: bwa index reference/ref.fa
+[main] Real time: 0.009 sec; CPU: 0.003 sec
+
+### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
+
+
+### ln -sf reference/ref.fa .
+
+
+### ln -sf reference/ref.fa.fai .
+
+
+### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
+
+
+### bwa mem  -Y -M -R '@RG\tID:b_out_dev\tSM:b_out_dev' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.9396. -r -s - - > snps.bam
+
+READ 10 WRITTEN 10 
+EXCLUDED 0 EXAMINED 10
+PAIRED 10 SINGLE 0
+DULPICATE PAIR 0 DUPLICATE SINGLE 0
+DUPLICATE TOTAL 0
+
+### samtools index snps.bam
+
+
+### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
+
+
+### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
+
+
+### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
+
+
+### cp snps.filt.vcf snps.vcf
+
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
+
+Loading reference: reference/ref.fa
+Loaded 1 sequences.
+Loading features: reference/ref.gff
+Parsing variants: snps.vcf
+Converted 1 SNPs to TAB format.
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
+
+
+### bcftools convert -Oz -o snps.vcf.gz snps.vcf
+
+
+### bcftools index -f snps.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
+
+
+### bcftools index -f snps.subs.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
+
+### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
+
+### samtools faidx reference/ref.fa
+
+
+### bwa index reference/ref.fa
+
+[bwa_index] Pack FASTA... 0.00 sec
+[bwa_index] Construct BWT for the packed sequence...
+[bwa_index] 0.00 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... 0.00 sec
+[main] Version: 0.7.17-r1188
+[main] CMD: bwa index reference/ref.fa
+[main] Real time: 0.008 sec; CPU: 0.002 sec
+
+### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
+
+
+### ln -sf reference/ref.fa .
+
+
+### ln -sf reference/ref.fa.fai .
+
+
+### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
+
+
+### bwa mem  -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.10001. -r -s - - > snps.bam
+
+READ 10 WRITTEN 10 
+EXCLUDED 0 EXAMINED 10
+PAIRED 10 SINGLE 0
+DULPICATE PAIR 0 DUPLICATE SINGLE 0
+DUPLICATE TOTAL 0
+
+### samtools index snps.bam
+
+
+### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
+
+
+### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
+
+
+### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
+
+
+### cp snps.filt.vcf snps.vcf
+
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
+
+Loading reference: reference/ref.fa
+Loaded 1 sequences.
+Loading features: reference/ref.gff
+Parsing variants: snps.vcf
+Converted 1 SNPs to TAB format.
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
+
+
+### bcftools convert -Oz -o snps.vcf.gz snps.vcf
+
+
+### bcftools index -f snps.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
+
+
+### bcftools index -f snps.subs.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
+
+### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
+
+### samtools faidx reference/ref.fa
+
+
+### bwa index reference/ref.fa
+
+[bwa_index] Pack FASTA... 0.00 sec
+[bwa_index] Construct BWT for the packed sequence...
+[bwa_index] 0.00 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... 0.00 sec
+[main] Version: 0.7.17-r1188
+[main] CMD: bwa index reference/ref.fa
+[main] Real time: 0.009 sec; CPU: 0.003 sec
+
+### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
+
+
+### ln -sf reference/ref.fa .
+
+
+### ln -sf reference/ref.fa.fai .
+
+
+### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
+
+
+### bwa mem  -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22109. -r -s - - > snps.bam
+
+READ 10 WRITTEN 10 
+EXCLUDED 0 EXAMINED 10
+PAIRED 10 SINGLE 0
+DULPICATE PAIR 0 DUPLICATE SINGLE 0
+DUPLICATE TOTAL 0
+
+### samtools index snps.bam
+
+
+### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
+
+
+### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
+
+
+### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
+
+
+### cp snps.filt.vcf snps.vcf
+
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
+
+Loading reference: reference/ref.fa
+Loaded 1 sequences.
+Loading features: reference/ref.gff
+Parsing variants: snps.vcf
+Converted 1 SNPs to TAB format.
+
+### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
+
+
+### bcftools convert -Oz -o snps.vcf.gz snps.vcf
+
+
+### bcftools index -f snps.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
+
+
+### bcftools index -f snps.subs.vcf.gz
+
+
+### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
+
+Note: the --sample option not given, applying all records regardless of the genotype
+
+### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
+