snps.tab file not created

[jennifercalawa]

Hello, I am trying to run snippy-multi on a MacBook Pro M2 and am running into an error. Here is the snps log output:

cd /Users/jennifercalawa/Desktop/FASTAforRoary/FNAonly

/Users/jennifercalawa/anaconda3/envs/snippyenv/bin/snippy --outdir CM1.1 --ctgs /Users/jennifercalawa/Desktop/FASTAforRoary/FNAonly/ncbi_dataset/CM1.1/CM1.1.fna --ref Vfischeri_ES114.all.gbk --cpus 6

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.04 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.93 seconds elapse. [bwa_index] Update BWT... 0.03 sec [bwa_index] Pack forward-only FASTA... 0.03 sec [bwa_index] Construct SA from BWT and Occ... 0.30 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 1.329 sec; CPU: 1.330 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

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 -v 2 -M -R '@RG\tID:snps\tSM:snps' -t 6 reference/ref.fa fake_reads.fq | samtools view -u -T reference/ref.fa -F 3844 -q 60 | samtools sort --reference reference/ref.fa > snps.bam)

[main] Version: 0.7.17-r1188 [main] CMD: bwa mem -v 2 -M -R @RG\tID:snps\tSM:snps -t 6 reference/ref.fa fake_reads.fq [main] Real time: 16.675 sec; CPU: 92.473 sec

samtools index snps.bam

samtools depth -aa -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 181047 > reference/ref.txt

freebayes-parallel reference/ref.txt 6 -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam > snps.raw.vcf

env: python: No such file or directory

And the terminal output says there is no .tab file (what I think is meant to be snps.tab) in my output folder. From what I can tell, all the other output files are being made, but the snps VCF is empty. Any help is greatly appreciated!