Error running snippy

[AlbaMunozSanta]

Hello everyone,

I am running snippy typing:

snippy --cpus 5 --outdir var --ref sequence.gb --pe1 R1_trimmed.fastq.gz --pe2 R2_trimmed.fastq.gz

Receiving this error: Error running command, check var/snps.log

When I check this file:

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: 0.002 sec

mkdir reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa

mkdir reference/ref && bgzip -c reference/ref.gff > reference/ref/genes.gff.gz

(bwa mem -v 2 -M -R '@rg ID:snps SM:snps' -t 5 reference/ref.fa fake_reads.fq | samtools view -@ 5 -F 3844 -q 60 -S -b -u -T reference/ref.fa - | samtools sort -O bam -o snps.bam -@ 5 -)

[E::bwa_set_rg] the read group line contained literal characters -- replace with escaped tabs: \t

samtools index snps.bam

samtools depth -q 20 snps.bam | bgzip > snps.depth.gz

tabix -s 1 -b 2 -e 2 snps.depth.gz

fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt

freebayes-parallel reference/ref.txt 5 -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf

Does someone know how to solve? I guess there is something wrong with the installation of snippy, but typing snippy --check and snippy --help, everything seems to be ok.

Thank you very much,

Regards,

Alba