Trim reads for Snippy?

[liuxianghui]

I trimmed the reads using trimmomatic first and tried to run Snippy. However, I am surprised to find out the snippy does not take both paired-end reads and unpaired ones together. It says "Can not mix read file types. Either (1) --R1 (2) --se (3) --peil (4) --ctgs (5) --bam" However, I do not want to discard the un-paired reads because there are quite a lot. (See the trimmomatic resut: Input Read Pairs: 687438 Both Surviving: 509184 (74.07%) Forward Only Surviving: 157556 (22.92%) Reverse Only Surviving: 5313 (0.77%) Dropped: 15385 (2.24%)) Is it a better way that I try to merge the paired end reads and do the trim and supply them as --se for snippy? I did not find similar question posted before.... Did you guys not trim raw reads before supply to snippy? Please kindly suggest, Xianghui

Here is the error messge. /gpfs0/scratch/xianghui/software/snippy-4.6.0/bin/snippy --outdir acrA_S15_mysnps --reference GCA_004355105.1_ASM435510v1_genomic.fasta --R1 acrA_S15_R1_paired.fq.gz --R2 acrA_S15_R2_paired.fq.gz --se acrA_S15_R1_unpaired.fq.gz, acrA_S15_R2_unpaired.fq.gz [14:58:17] This is snippy 4.6.0 [14:58:17] Written by Torsten Seemann [14:58:17] Obtained from https://github.com/tseemann/snippy [14:58:17] Detected operating system: linux [14:58:17] Enabling bundled linux tools. [14:58:17] Found bwa - /home/xianghui/anaconda3/bin/bwa [14:58:17] Found bcftools - /gpfs0/scratch/xianghui/software/bcftools-1.9/bcftools [14:58:17] Found samtools - /gpfs0/scratch/xianghui/software/samtools-1.9/samtools [14:58:17] Found java - /home/xianghui/anaconda3/bin/java [14:58:17] Found snpEff - /gpfs0/scratch/xianghui/software/snippy-4.6.0/binaries/noarch/snpEff [14:58:17] Found samclip - /gpfs0/scratch/xianghui/software/snippy-4.6.0/binaries/noarch/samclip [14:58:17] Found seqtk - /home/xianghui/software/bin/seqtk [14:58:17] Found parallel - /home/xianghui/anaconda3/bin/parallel [14:58:17] Found freebayes - /home/xianghui/anaconda3/bin/freebayes [14:58:17] Found freebayes-parallel - /home/xianghui/anaconda3/bin/freebayes-parallel [14:58:17] Found fasta_generate_regions.py - /home/xianghui/anaconda3/bin/fasta_generate_regions.py [14:58:17] Found vcfstreamsort - /home/xianghui/anaconda3/bin/vcfstreamsort [14:58:17] Found vcfuniq - /home/xianghui/anaconda3/bin/vcfuniq [14:58:17] Found vcffirstheader - /home/xianghui/anaconda3/bin/vcffirstheader [14:58:17] Found gzip - /usr/bin/gzip [14:58:17] Found vt - /gpfs0/scratch/xianghui/software/snippy-4.6.0/binaries/linux/vt [14:58:17] Found snippy-vcf_to_tab - /gpfs0/scratch/xianghui/software/snippy-4.6.0/bin/snippy-vcf_to_tab [14:58:18] Found snippy-vcf_report - /gpfs0/scratch/xianghui/software/snippy-4.6.0/bin/snippy-vcf_report [14:58:18] Checking version: samtools --version is >= 1.7 - ok, have 1.9 [14:58:18] Checking version: bcftools --version is >= 1.7 - ok, have 1.9 [14:58:18] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.2 [14:58:18] Checking version: snpEff -version is >= 4.3 - ok, have 4.3 [14:58:18] Checking version: bwa is >= 0.7.12 - ok, have 0.7.17 [14:58:18] Using reference: /gpfs0/scratch/xianghui/software/Oishi/GCA_004355105.1_ASM435510v1_genomic.fasta [14:58:18] Treating reference as 'fasta' format. [14:58:18] Will use 8 CPU cores. [14:58:18] Can not mix read file types. Either (1) --R1 (2) --se (3) --peil (4) --ctgs (5) --bam