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Here is my terminal log: (myenv) hp@imran:$ cd /home/hp/Desktop/Snippy (myenv) hp@imran:/Desktop/Snippy$ snippy --cpus 8 --outdir kill --ref free.gbk --R1 76_S76_R1_001.fastq.gz --R2 76_S76_R2_001.fastq.gz [21:32:10] This is snippy 4.6.0 [21:32:10] Written by Torsten Seemann [21:32:10] Obtained from https://github.com/tseemann/snippy [21:32:10] Detected operating system: linux [21:32:10] Enabling bundled linux tools. [21:32:10] Found bwa - /home/hp/anaconda3/envs/myenv/bin/bwa [21:32:10] Found bcftools - /home/hp/anaconda3/envs/myenv/bin/bcftools [21:32:10] Found samtools - /home/hp/anaconda3/envs/myenv/bin/samtools [21:32:10] Found java - /home/hp/anaconda3/envs/myenv/bin/java [21:32:10] Found snpEff - /home/hp/anaconda3/envs/myenv/bin/snpEff [21:32:10] Found samclip - /home/hp/anaconda3/envs/myenv/bin/samclip [21:32:10] Found seqtk - /home/hp/anaconda3/envs/myenv/bin/seqtk [21:32:10] Found parallel - /home/hp/anaconda3/envs/myenv/bin/parallel [21:32:10] Found freebayes - /home/hp/anaconda3/envs/myenv/bin/freebayes [21:32:10] Found freebayes-parallel - /home/hp/anaconda3/envs/myenv/bin/freebayes-parallel [21:32:10] Found fasta_generate_regions.py - /home/hp/anaconda3/envs/myenv/bin/fasta_generate_regions.py [21:32:10] Found vcfstreamsort - /home/hp/anaconda3/envs/myenv/bin/vcfstreamsort [21:32:10] Found vcfuniq - /home/hp/anaconda3/envs/myenv/bin/vcfuniq [21:32:10] Found vcffirstheader - /home/hp/anaconda3/envs/myenv/bin/vcffirstheader [21:32:10] Found gzip - /usr/bin/gzip [21:32:10] Found vt - /home/hp/anaconda3/envs/myenv/bin/vt [21:32:10] Found snippy-vcf_to_tab - /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_to_tab [21:32:10] Found snippy-vcf_report - /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_report [21:32:10] Checking version: samtools --version is >= 1.7 - ok, have 1.20 [21:32:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 [21:32:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6 [21:32:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [21:32:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 [21:32:10] Using reference: /home/hp/Desktop/Snippy/free.gbk [21:32:10] Treating reference as 'genbank' format. [21:32:10] Will use 8 CPU cores. [21:32:10] Using read file: /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz [21:32:10] Using read file: /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz [21:32:10] Creating folder: kill [21:32:10] Changing working directory: kill [21:32:10] Creating reference folder: reference [21:32:10] Extracting FASTA and GFF from reference. [21:32:11] Wrote 2 sequences to ref.fa [21:32:11] Wrote 4738 features to ref.gff [21:32:11] Creating reference/snpeff.config [21:32:11] Freebayes will process 15 chunks of 350130 bp, 8 chunks at a time. [21:32:11] Using BAM RG (Read Group) ID: kill [21:32:11] Running: samtools faidx reference/ref.fa 2>> snps.log [21:32:11] Running: bwa index reference/ref.fa 2>> snps.log [21:32:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [21:32:13] Running: ln -sf reference/ref.fa . 2>> snps.log [21:32:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [21:32:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [21:32:13] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [21:32:18] Running: bwa mem -Y -M -R '@rg\tID:kill\tSM:kill' -t 8 reference/ref.fa /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | samtools markdup -T /tmp --threads 3 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 2 sequences in reference/ref.fa.fai [M::process] read 556792 sequences (80000187 bp)... [M::process] read 556588 sequences (80000094 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 249595, 38, 2) [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: (200, 280, 368) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 704) [M::mem_pestat] mean and std.dev: (288.83, 130.50) [M::mem_pestat] low and high boundaries for proper pairs: (1, 872) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (240, 1449, 3692) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10596) [M::mem_pestat] mean and std.dev: (1896.63, 1652.53) [M::mem_pestat] low and high boundaries for proper pairs: (1, 14048) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 556792 reads in 86.218 CPU sec, 10.876 real sec [samclip] Processed 100000 records... [samclip] Processed 200000 records... [samclip] Processed 300000 records... [samclip] Processed 400000 records... [samclip] Processed 500000 records... [M::process] read 556932 sequences (80000027 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 249657, 37, 5) [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: (200, 280, 369) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707) [M::mem_pestat] mean and std.dev: (288.91, 130.63) [M::mem_pestat] low and high boundaries for proper pairs: (1, 876) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (693, 2139, 3596) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9402) [M::mem_pestat] mean and std.dev: (2244.54, 1900.18) [M::mem_pestat] low and high boundaries for proper pairs: (1, 12305) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 556588 reads in 96.613 CPU sec, 12.732 real sec [samclip] Processed 600000 records... [samclip] Processed 700000 records... [samclip] Processed 800000 records... [samclip] Processed 900000 records... [samclip] Processed 1000000 records... [samclip] Processed 1100000 records... [M::process] read 559580 sequences (80000154 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 249406, 45, 6) [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: (199, 278, 367) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 703) [M::mem_pestat] mean and std.dev: (287.82, 130.46) [M::mem_pestat] low and high boundaries for proper pairs: (1, 871) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (353, 1200, 3772) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10610) [M::mem_pestat] mean and std.dev: (2422.64, 2763.86) [M::mem_pestat] low and high boundaries for proper pairs: (1, 14029) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 556932 reads in 98.350 CPU sec, 13.000 real sec [samclip] Processed 1200000 records... [samclip] Processed 1300000 records... [samclip] Processed 1400000 records... [samclip] Processed 1500000 records... [samclip] Processed 1600000 records... [M::process] read 559578 sequences (80000168 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 250720, 40, 4) [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: (194, 272, 357) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683) [M::mem_pestat] mean and std.dev: (279.40, 126.16) [M::mem_pestat] low and high boundaries for proper pairs: (1, 846) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (309, 1027, 3162) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8868) [M::mem_pestat] mean and std.dev: (1704.60, 1577.68) [M::mem_pestat] low and high boundaries for proper pairs: (1, 11721) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 559580 reads in 96.621 CPU sec, 12.767 real sec [samclip] Processed 1700000 records... [samclip] Processed 1800000 records... [samclip] Processed 1900000 records... [samclip] Processed 2000000 records... [samclip] Processed 2100000 records... [samclip] Processed 2200000 records... [M::process] read 410586 sequences (58696297 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 251187, 51, 4) [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: (193, 273, 358) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688) [M::mem_pestat] mean and std.dev: (280.27, 126.97) [M::mem_pestat] low and high boundaries for proper pairs: (1, 853) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (1044, 2564, 3928) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9696) [M::mem_pestat] mean and std.dev: (2506.67, 1754.01) [M::mem_pestat] low and high boundaries for proper pairs: (1, 12580) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 559578 reads in 97.271 CPU sec, 13.004 real sec [samclip] Processed 2300000 records... [samclip] Processed 2400000 records... [samclip] Processed 2500000 records... [samclip] Processed 2600000 records... [samclip] Processed 2700000 records... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 183985, 28, 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: (193, 272, 357) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685) [M::mem_pestat] mean and std.dev: (279.56, 126.44) [M::mem_pestat] low and high boundaries for proper pairs: (1, 849) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (248, 2948, 6154) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17966) [M::mem_pestat] mean and std.dev: (3266.71, 2977.52) [M::mem_pestat] low and high boundaries for proper pairs: (1, 23872) [M::mem_pestat] skip orientation RR as there are not enough pairs [M::mem_pestat] skip orientation RF [M::mem_process_seqs] Processed 410586 reads in 74.558 CPU sec, 10.055 real sec [samclip] Processed 2800000 records... [samclip] Processed 2900000 records... [samclip] Processed 3000000 records... [samclip] Processed 3100000 records... [samclip] Processed 3200000 records... [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @rg\tID:kill\tSM:kill -t 8 reference/ref.fa /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz [main] Real time: 74.729 sec; CPU: 550.926 sec [samclip] Total SAM records 3202790, removed 68965, allowed 45067, passed 3133825 [samclip] Header contained 5 lines [samclip] Done. [bam_sort_core] merging from 0 files and 3 in-memory blocks... [bam_sort_core] merging from 0 files and 3 in-memory blocks... [21:33:53] Running: samtools index snps.bam 2>> snps.log [21:33:54] Running: fasta_generate_regions.py reference/ref.fa.fai 350130 > reference/ref.txt 2>> snps.log [21:33:54] Running: freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log [21:34:39] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' 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 2>> snps.log normalize v0.5
options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [n] no fail on reference inconsistency for non SNPs false [q] quiet false [d] debug false [r] reference FASTA file reference/ref.fa
[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_004603.1:558-562 FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file [21:34:39] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf 2>> snps.log [21:34:40] Running: /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log [21:34:42] Running: /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log [21:34:42] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log [21:34:42] Running: bcftools index -f snps.vcf.gz 2>> snps.log [21:34:42] Running: bcftools consensus --sample kill -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log [21:34:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log [21:34:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log [21:34:42] Running: bcftools consensus --sample kill -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log [21:34:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log [21:34:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa [21:34:47] Marked 1690 heterozygous sites with 'n' [21:34:47] Creating extra output files: BED GFF CSV TXT HTML [21:34:47] Identified 0 variants. [21:34:47] Result folder: kill [21:34:47] Result files: [21:34:47] * kill/snps.aligned.fa [21:34:47] * kill/snps.bam [21:34:47] * kill/snps.bam.bai [21:34:47] * kill/snps.bed [21:34:47] * kill/snps.consensus.fa [21:34:47] * kill/snps.consensus.subs.fa [21:34:47] * kill/snps.csv [21:34:47] * kill/snps.filt.vcf [21:34:47] * kill/snps.gff [21:34:47] * kill/snps.html [21:34:47] * kill/snps.log [21:34:47] * kill/snps.raw.vcf [21:34:47] * kill/snps.subs.vcf [21:34:47] * kill/snps.tab [21:34:47] * kill/snps.txt [21:34:47] * kill/snps.vcf [21:34:47] * kill/snps.vcf.gz [21:34:47] * kill/snps.vcf.gz.csi [21:34:47] Walltime used: 2 minutes, 37 seconds [21:34:47] May the SNPs be with yo
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Here is my terminal log:
(myenv) hp@imran:
$ cd /home/hp/Desktop/Snippy/Desktop/Snippy$ snippy --cpus 8 --outdir kill --ref free.gbk --R1 76_S76_R1_001.fastq.gz --R2 76_S76_R2_001.fastq.gz(myenv) hp@imran:
[21:32:10] This is snippy 4.6.0
[21:32:10] Written by Torsten Seemann
[21:32:10] Obtained from https://github.com/tseemann/snippy
[21:32:10] Detected operating system: linux
[21:32:10] Enabling bundled linux tools.
[21:32:10] Found bwa - /home/hp/anaconda3/envs/myenv/bin/bwa
[21:32:10] Found bcftools - /home/hp/anaconda3/envs/myenv/bin/bcftools
[21:32:10] Found samtools - /home/hp/anaconda3/envs/myenv/bin/samtools
[21:32:10] Found java - /home/hp/anaconda3/envs/myenv/bin/java
[21:32:10] Found snpEff - /home/hp/anaconda3/envs/myenv/bin/snpEff
[21:32:10] Found samclip - /home/hp/anaconda3/envs/myenv/bin/samclip
[21:32:10] Found seqtk - /home/hp/anaconda3/envs/myenv/bin/seqtk
[21:32:10] Found parallel - /home/hp/anaconda3/envs/myenv/bin/parallel
[21:32:10] Found freebayes - /home/hp/anaconda3/envs/myenv/bin/freebayes
[21:32:10] Found freebayes-parallel - /home/hp/anaconda3/envs/myenv/bin/freebayes-parallel
[21:32:10] Found fasta_generate_regions.py - /home/hp/anaconda3/envs/myenv/bin/fasta_generate_regions.py
[21:32:10] Found vcfstreamsort - /home/hp/anaconda3/envs/myenv/bin/vcfstreamsort
[21:32:10] Found vcfuniq - /home/hp/anaconda3/envs/myenv/bin/vcfuniq
[21:32:10] Found vcffirstheader - /home/hp/anaconda3/envs/myenv/bin/vcffirstheader
[21:32:10] Found gzip - /usr/bin/gzip
[21:32:10] Found vt - /home/hp/anaconda3/envs/myenv/bin/vt
[21:32:10] Found snippy-vcf_to_tab - /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_to_tab
[21:32:10] Found snippy-vcf_report - /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_report
[21:32:10] Checking version: samtools --version is >= 1.7 - ok, have 1.20
[21:32:10] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
[21:32:10] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6
[21:32:10] Checking version: snpEff -version is >= 4.3 - ok, have 5.0
[21:32:10] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
[21:32:10] Using reference: /home/hp/Desktop/Snippy/free.gbk
[21:32:10] Treating reference as 'genbank' format.
[21:32:10] Will use 8 CPU cores.
[21:32:10] Using read file: /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz
[21:32:10] Using read file: /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz
[21:32:10] Creating folder: kill
[21:32:10] Changing working directory: kill
[21:32:10] Creating reference folder: reference
[21:32:10] Extracting FASTA and GFF from reference.
[21:32:11] Wrote 2 sequences to ref.fa
[21:32:11] Wrote 4738 features to ref.gff
[21:32:11] Creating reference/snpeff.config
[21:32:11] Freebayes will process 15 chunks of 350130 bp, 8 chunks at a time.
[21:32:11] Using BAM RG (Read Group) ID: kill
[21:32:11] Running: samtools faidx reference/ref.fa 2>> snps.log
[21:32:11] Running: bwa index reference/ref.fa 2>> snps.log
[21:32:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
[21:32:13] Running: ln -sf reference/ref.fa . 2>> snps.log
[21:32:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
[21:32:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
[21:32:13] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log
[21:32:18] Running: bwa mem -Y -M -R '@rg\tID:kill\tSM:kill' -t 8 reference/ref.fa /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /tmp --threads 3 -m 2000M | samtools markdup -T /tmp --threads 3 -r -s - - > snps.bam 2>> snps.log
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
[samclip] Loading: reference/ref.fa.fai
[samclip] Found 2 sequences in reference/ref.fa.fai
[M::process] read 556792 sequences (80000187 bp)...
[M::process] read 556588 sequences (80000094 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 249595, 38, 2)
[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: (200, 280, 368)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 704)
[M::mem_pestat] mean and std.dev: (288.83, 130.50)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 872)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (240, 1449, 3692)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10596)
[M::mem_pestat] mean and std.dev: (1896.63, 1652.53)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 14048)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 556792 reads in 86.218 CPU sec, 10.876 real sec
[samclip] Processed 100000 records...
[samclip] Processed 200000 records...
[samclip] Processed 300000 records...
[samclip] Processed 400000 records...
[samclip] Processed 500000 records...
[M::process] read 556932 sequences (80000027 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 249657, 37, 5)
[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: (200, 280, 369)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 707)
[M::mem_pestat] mean and std.dev: (288.91, 130.63)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 876)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (693, 2139, 3596)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9402)
[M::mem_pestat] mean and std.dev: (2244.54, 1900.18)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 12305)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 556588 reads in 96.613 CPU sec, 12.732 real sec
[samclip] Processed 600000 records...
[samclip] Processed 700000 records...
[samclip] Processed 800000 records...
[samclip] Processed 900000 records...
[samclip] Processed 1000000 records...
[samclip] Processed 1100000 records...
[M::process] read 559580 sequences (80000154 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 249406, 45, 6)
[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: (199, 278, 367)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 703)
[M::mem_pestat] mean and std.dev: (287.82, 130.46)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 871)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (353, 1200, 3772)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10610)
[M::mem_pestat] mean and std.dev: (2422.64, 2763.86)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 14029)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 556932 reads in 98.350 CPU sec, 13.000 real sec
[samclip] Processed 1200000 records...
[samclip] Processed 1300000 records...
[samclip] Processed 1400000 records...
[samclip] Processed 1500000 records...
[samclip] Processed 1600000 records...
[M::process] read 559578 sequences (80000168 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 250720, 40, 4)
[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: (194, 272, 357)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 683)
[M::mem_pestat] mean and std.dev: (279.40, 126.16)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 846)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (309, 1027, 3162)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 8868)
[M::mem_pestat] mean and std.dev: (1704.60, 1577.68)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 11721)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 559580 reads in 96.621 CPU sec, 12.767 real sec
[samclip] Processed 1700000 records...
[samclip] Processed 1800000 records...
[samclip] Processed 1900000 records...
[samclip] Processed 2000000 records...
[samclip] Processed 2100000 records...
[samclip] Processed 2200000 records...
[M::process] read 410586 sequences (58696297 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (5, 251187, 51, 4)
[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: (193, 273, 358)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 688)
[M::mem_pestat] mean and std.dev: (280.27, 126.97)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 853)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (1044, 2564, 3928)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 9696)
[M::mem_pestat] mean and std.dev: (2506.67, 1754.01)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 12580)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 559578 reads in 97.271 CPU sec, 13.004 real sec
[samclip] Processed 2300000 records...
[samclip] Processed 2400000 records...
[samclip] Processed 2500000 records...
[samclip] Processed 2600000 records...
[samclip] Processed 2700000 records...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (2, 183985, 28, 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: (193, 272, 357)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 685)
[M::mem_pestat] mean and std.dev: (279.56, 126.44)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 849)
[M::mem_pestat] analyzing insert size distribution for orientation RF...
[M::mem_pestat] (25, 50, 75) percentile: (248, 2948, 6154)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 17966)
[M::mem_pestat] mean and std.dev: (3266.71, 2977.52)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 23872)
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_pestat] skip orientation RF
[M::mem_process_seqs] Processed 410586 reads in 74.558 CPU sec, 10.055 real sec
[samclip] Processed 2800000 records...
[samclip] Processed 2900000 records...
[samclip] Processed 3000000 records...
[samclip] Processed 3100000 records...
[samclip] Processed 3200000 records...
[main] Version: 0.7.18-r1243-dirty
[main] CMD: bwa mem -Y -M -R @rg\tID:kill\tSM:kill -t 8 reference/ref.fa /home/hp/Desktop/Snippy/76_S76_R1_001.fastq.gz /home/hp/Desktop/Snippy/76_S76_R2_001.fastq.gz
[main] Real time: 74.729 sec; CPU: 550.926 sec
[samclip] Total SAM records 3202790, removed 68965, allowed 45067, passed 3133825
[samclip] Header contained 5 lines
[samclip] Done.
[bam_sort_core] merging from 0 files and 3 in-memory blocks...
[bam_sort_core] merging from 0 files and 3 in-memory blocks...
[21:33:53] Running: samtools index snps.bam 2>> snps.log
[21:33:54] Running: fasta_generate_regions.py reference/ref.fa.fai 350130 > reference/ref.txt 2>> snps.log
[21:33:54] Running: freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[21:34:39] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' 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 2>> snps.log
normalize v0.5
options: input VCF file -
[o] output VCF file -
[w] sorting window size 10000
[n] no fail on reference inconsistency for non SNPs false
[q] quiet false
[d] debug false
[r] reference FASTA file reference/ref.fa
[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: NC_004603.1:558-562
FAQ: http://genome.sph.umich.edu/wiki/Vt#1._vt_cannot_retrieve_sequences_from_my_reference_sequence_file
[21:34:39] Running: snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf 2>> snps.log
[21:34:40] Running: /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
[21:34:42] Running: /home/hp/anaconda3/envs/myenv/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
[21:34:42] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
[21:34:42] Running: bcftools index -f snps.vcf.gz 2>> snps.log
[21:34:42] Running: bcftools consensus --sample kill -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
[21:34:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
[21:34:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
[21:34:42] Running: bcftools consensus --sample kill -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
[21:34:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
[21:34:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
[21:34:47] Marked 1690 heterozygous sites with 'n'
[21:34:47] Creating extra output files: BED GFF CSV TXT HTML
[21:34:47] Identified 0 variants.
[21:34:47] Result folder: kill
[21:34:47] Result files:
[21:34:47] * kill/snps.aligned.fa
[21:34:47] * kill/snps.bam
[21:34:47] * kill/snps.bam.bai
[21:34:47] * kill/snps.bed
[21:34:47] * kill/snps.consensus.fa
[21:34:47] * kill/snps.consensus.subs.fa
[21:34:47] * kill/snps.csv
[21:34:47] * kill/snps.filt.vcf
[21:34:47] * kill/snps.gff
[21:34:47] * kill/snps.html
[21:34:47] * kill/snps.log
[21:34:47] * kill/snps.raw.vcf
[21:34:47] * kill/snps.subs.vcf
[21:34:47] * kill/snps.tab
[21:34:47] * kill/snps.txt
[21:34:47] * kill/snps.vcf
[21:34:47] * kill/snps.vcf.gz
[21:34:47] * kill/snps.vcf.gz.csi
[21:34:47] Walltime used: 2 minutes, 37 seconds
[21:34:47] May the SNPs be with yo
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