A Problem

[xialei012]

I have some problems. When using snippy, gbk file and fasta file, are downloaded from NCBI. The code is as follows: snippy --outdir test1 --ref test.gbk --ctgs test.fa [14:47:23] This is snippy 4.6.0 [14:47:23] Written by Torsten Seemann [14:47:23] Obtained from https://github.com/tseemann/snippy [14:47:23] Detected operating system: linux [14:47:23] Enabling bundled linux tools. [14:47:23] Found bwa - /gss1/home/chenjf01/a/bin/bwa [14:47:23] Found bcftools - /gss1/home/chenjf01/a/bin/bcftools [14:47:23] Found samtools - /gss1/home/chenjf01/a/bin/samtools [14:47:23] Found java - /gss1/home/chenjf01/a/bin/java [14:47:23] Found snpEff - /gss1/home/chenjf01/a/bin/snpEff [14:47:23] Found samclip - /gss1/home/chenjf01/a/bin/samclip [14:47:23] Found seqtk - /gss1/home/chenjf01/a/bin/seqtk [14:47:23] Found parallel - /gss1/home/chenjf01/a/bin/parallel [14:47:23] Found freebayes - /gss1/home/chenjf01/a/bin/freebayes [14:47:23] Found freebayes-parallel - /gss1/home/chenjf01/a/bin/freebayes-parallel [14:47:23] Found fasta_generate_regions.py - /gss1/home/chenjf01/a/bin/fasta_generate_regions.py [14:47:23] Found vcfstreamsort - /gss1/home/chenjf01/a/bin/vcfstreamsort [14:47:23] Found vcfuniq - /gss1/home/chenjf01/a/bin/vcfuniq [14:47:23] Found vcffirstheader - /gss1/home/chenjf01/a/bin/vcffirstheader [14:47:23] Found gzip - /bin/gzip [14:47:23] Found vt - /gss1/home/chenjf01/a/bin/vt [14:47:23] Found snippy-vcf_to_tab - /gss1/home/chenjf01/a/bin/snippy-vcf_to_tab [14:47:23] Found snippy-vcf_report - /gss1/home/chenjf01/a/bin/snippy-vcf_report [14:47:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.9 [14:47:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:47:24] Checking version: snpEff -version is >= 4.3 - ok, have 5.0 [14:47:24] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:47:24] Using reference: /gss1/home/chenjf01/wh/test.gbk [14:47:24] Treating reference as 'genbank' format. [14:47:24] Will use 8 CPU cores. [14:47:24] Using read file: /gss1/home/chenjf01/wh/test.fa [14:47:24] Creating folder: test1 [14:47:24] Changing working directory: test1 [14:47:24] Creating reference folder: reference [14:47:24] Extracting FASTA and GFF from reference. [14:47:24] Wrote 3 sequences to ref.fa [14:47:24] Wrote 300 features to ref.gff [14:47:24] Shredding /gss1/home/chenjf01/wh/test.fa into pseudo-reads [14:47:24] Wrote 25510 fake 250bp reads (20x, stride 25bp) to fake_reads.fq [14:47:24] Creating reference/snpeff.config [14:47:24] Freebayes will process 15 chunks of 21517 bp, 8 chunks at a time. [14:47:24] Using BAM RG (Read Group) ID: test1 [14:47:24] Running: samtools faidx reference/ref.fa 2>> snps.log [14:47:24] Running: bwa index reference/ref.fa 2>> snps.log [14:47:25] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log [14:47:25] Running: ln -sf reference/ref.fa . 2>> snps.log [14:47:25] Running: ln -sf reference/ref.fa.fai . 2>> snps.log [14:47:25] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log [14:47:25] Running: snpEff build -c reference/snpeff.config -dataDir . -gff3 ref 2>> snps.log [14:47:28] Running: bwa mem -Y -M -R '@RG\tID:test1\tSM:test1' -t 8 reference/ref.fa fake_reads.fq | 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 sort: invalid option -- 'T' sort: invalid option -- '-' sort: invalid option -- 't' sort: invalid option -- 'h' sort: invalid option -- 'r' sort: invalid option -- 'e' sort: invalid option -- 'a' sort: invalid option -- 'd' sort: invalid option -- 's' [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). sort: invalid option -- 'T' sort: invalid option -- '-' sort: invalid option -- 't' fixmate: invalid option -- 'm' sort: invalid option -- 'h' sort: invalid option -- 'r' fixmate: invalid option -- '-' sort: invalid option -- 'e' fixmate: invalid option -- 't' sort: invalid option -- 'a' fixmate: invalid option -- 'h' sort: invalid option -- 'd' fixmate: invalid option -- 'e' sort: invalid option -- 's' fixmate: invalid option -- 'a' fixmate: invalid option -- 'd' fixmate: invalid option -- 's' [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). open: No such file or directory [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 3 sequences in reference/ref.fa.fai [M::process] read 25510 sequences (6377500 bp)... [M::mem_process_seqs] Processed 25510 reads in 2.189 CPU sec, 0.295 real sec [14:47:28] Error running command, check test1/snps.log