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tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
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dyld: Symbol not found: __ZNKSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE13find_first_ofEPKcm - Failed to read from standard input: unknown file type #510

Open jellyvanderwoude opened 2 years ago

jellyvanderwoude commented 2 years ago

My code and printed output:

(base) bio-24046:~ jvanderwoude3$ snippy --outdir trial --ref PAO1.gbk --R1 CF1_LeftLower_D12_R1.fastq.gz --R2 CF1_LeftLower_D12_R2.fastq.gz [12:13:56] This is snippy 4.6.0 [12:13:56] Written by Torsten Seemann [12:13:56] Obtained from https://github.com/tseemann/snippy [12:13:56] Detected operating system: darwin [12:13:56] Enabling bundled darwin tools. [12:13:56] Found bwa - /usr/local/bin/bwa [12:13:56] Found bcftools - /usr/local/bin/bcftools [12:13:56] Found samtools - /usr/local/bin/samtools [12:13:56] Found java - /usr/bin/java [12:13:56] Found snpEff - /usr/local/bin/snpEff [12:13:56] Found samclip - /usr/local/bin/samclip [12:13:56] Found seqtk - /usr/local/bin/seqtk [12:13:56] Found parallel - /usr/local/bin/parallel [12:13:56] Found freebayes - /usr/local/bin/freebayes [12:13:56] Found freebayes-parallel - /usr/local/Cellar/snippy/4.6.0/binaries/noarch/freebayes-parallel [12:13:56] Found fasta_generate_regions.py - /usr/local/Cellar/snippy/4.6.0/binaries/noarch/fasta_generate_regions.py [12:13:56] Found vcfstreamsort - /usr/local/bin/vcfstreamsort [12:13:56] Found vcfuniq - /usr/local/bin/vcfuniq [12:13:56] Found vcffirstheader - /usr/local/bin/vcffirstheader [12:13:56] Found gzip - /usr/bin/gzip [12:13:56] Found vt - /usr/local/bin/vt [12:13:56] Found snippy-vcf_to_tab - /usr/local/Cellar/snippy/4.6.0/bin/snippy-vcf_to_tab [12:13:56] Found snippy-vcf_report - /usr/local/Cellar/snippy/4.6.0/bin/snippy-vcf_report [12:13:56] Checking version: samtools --version is >= 1.7 - ok, have 1.15 [12:13:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.15 [12:13:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.6 [12:13:56] Checking version: snpEff -version is >= 4.3 - ok, have 4.3 [12:13:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [12:13:56] Using reference: /Users/jvanderwoude3/PAO1.gbk [12:13:56] Treating reference as 'genbank' format. [12:13:56] Will use 8 CPU cores. [12:13:56] Using read file: /Users/jvanderwoude3/CF1_LeftLower_D12_R1.fastq.gz [12:13:56] Using read file: /Users/jvanderwoude3/CF1_LeftLower_D12_R2.fastq.gz [12:13:56] Creating folder: trial [12:13:56] Changing working directory: trial [12:13:56] Creating reference folder: reference [12:13:56] Extracting FASTA and GFF from reference. [12:13:59] Wrote 1 sequences to ref.fa [12:13:59] Wrote 5713 features to ref.gff [12:13:59] Creating reference/snpeff.config [12:13:59] Freebayes will process 15 chunks of 424592 bp, 8 chunks at a time. [12:13:59] Using BAM RG (Read Group) ID: trial [12:13:59] Running: samtools faidx reference/ref.fa 2>> snps.log [12:13:59] Running: bwa index reference/ref.fa 2>> snps.log [12:14:01] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [12:14:01] Running: ln -sf reference/ref.fa . 2>> snps.log [12:14:01] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [12:14:01] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [12:14:01] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [12:14:05] Running: bwa mem -Y -M -R '@RG\tID:trial\tSM:trial' -t 8 reference/ref.fa /Users/jvanderwoude3/CF1_LeftLower_D12_R1.fastq.gz /Users/jvanderwoude3/CF1_LeftLower_D12_R2.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -m 2000M | samtools markdup -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --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 1 sequences in reference/ref.fa.fai [M::process] read 828570 sequences (73856120 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (132, 297362, 126, 133) [M::mem_pestat] analyzing insert size distribution for orientation FF... [M::mem_pestat] (25, 50, 75) percentile: (328, 501, 922) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 2110) [M::mem_pestat] mean and std.dev: (486.71, 312.74) [M::mem_pestat] low and high boundaries for proper pairs: (1, 2704) [M::mem_pestat] analyzing insert size distribution for orientation FR... [M::mem_pestat] (25, 50, 75) percentile: (337, 456, 629) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1213) [M::mem_pestat] mean and std.dev: (496.04, 216.49) [M::mem_pestat] low and high boundaries for proper pairs: (1, 1505) [M::mem_pestat] analyzing insert size distribution for orientation RF... [M::mem_pestat] (25, 50, 75) percentile: (133, 1128, 3535) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 10339) [M::mem_pestat] mean and std.dev: (2248.12, 2781.25) [M::mem_pestat] low and high boundaries for proper pairs: (1, 13741) [M::mem_pestat] analyzing insert size distribution for orientation RR... [M::mem_pestat] (25, 50, 75) percentile: (304, 491, 809) [M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 1819) [M::mem_pestat] mean and std.dev: (452.31, 232.94) [M::mem_pestat] low and high boundaries for proper pairs: (1, 2324) [M::mem_pestat] skip orientation FF [M::mem_pestat] skip orientation RF [M::mem_pestat] skip orientation RR [M::mem_process_seqs] Processed 828570 reads in 31.228 CPU sec, 3.931 real sec [samclip] Processed 100000 records... [samclip] Processed 200000 records... [samclip] Processed 300000 records... [samclip] Processed 400000 records... [samclip] Processed 500000 records... [samclip] Processed 600000 records... [samclip] Processed 700000 records... [samclip] Processed 800000 records... [main] Version: 0.7.17-r1188 [main] CMD: bwa mem -Y -M -R @RG\tID:trial\tSM:trial -t 8 reference/ref.fa /Users/jvanderwoude3/CF1_LeftLower_D12_R1.fastq.gz /Users/jvanderwoude3/CF1_LeftLower_D12_R2.fastq.gz [main] Real time: 8.213 sec; CPU: 33.380 sec [samclip] Total SAM records 838680, removed 36347, allowed 10230, passed 802333 [samclip] Header contained 3 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... [12:14:19] Running: samtools index snps.bam 2>> snps.log [12:14:19] Running: fasta_generate_regions.py reference/ref.fa.fai 424592 > reference/ref.txt 2>> snps.log [12:14:20] 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 [12:14:24] 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 dyld: Symbol not found: ZNKSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEE13find_first_ofEPKcm Referenced from: /usr/local/bin/vt Expected in: /usr/lib/libstdc++.6.dylib in /usr/local/bin/vt [12:14:24] Error running command, check trial/snps.log

trial/snps.log output:

echo snippy 4.6.0

cd /Users/jvanderwoude3

/usr/local/bin/snippy --outdir trial --ref PAO1.gbk --R1 CF1_LeftLower_D12_R1.fastq.gz --R2 CF1_LeftLower_D12_R2.fastq.gz

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.05 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 1.50 seconds elapse. [bwa_index] Update BWT... 0.04 sec [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa_index] Construct SA from BWT and Occ... 0.40 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 2.020 sec; CPU: 2.016 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

snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

WARNING: All frames are zero! This seems rather odd, please check that 'frame' information in your 'genes' file is accurate.

bwa mem -Y -M -R '@RG\tID:trial\tSM:trial' -t 8 reference/ref.fa /Users/jvanderwoude3/CF1_LeftLower_D12_R1.fastq.gz /Users/jvanderwoude3/CF1_LeftLower_D12_R2.fastq.gz | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -m 2000M | samtools fixmate -m --threads 3 - - | samtools sort -l 0 -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -m 2000M | samtools markdup -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -r -s - - > snps.bam

COMMAND: samtools markdup -T /private/var/folders/qr/bwx01b092d3c1p5yq_4hrrhcz1glm0/T --threads 3 -r -s - - READ: 802333 WRITTEN: 792959 EXCLUDED: 127697 EXAMINED: 674636 PAIRED: 640604 SINGLE: 34032 DUPLICATE PAIR: 2956 DUPLICATE SINGLE: 6418 DUPLICATE PAIR OPTICAL: 0 DUPLICATE SINGLE OPTICAL: 0 DUPLICATE NON PRIMARY: 0 DUPLICATE NON PRIMARY OPTICAL: 0 DUPLICATE PRIMARY TOTAL: 9374 DUPLICATE TOTAL: 9374 ESTIMATED_LIBRARY_SIZE: 34599974

samtools index snps.bam

fasta_generate_regions.py reference/ref.fa.fai 424592 > reference/ref.txt

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

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

Failed to read from standard input: unknown file type

lilithfeer commented 2 years ago

@jellyvanderwoude I have the same issue. Did you manage to resolve it? Thank you very much in advance