Missing parentheses in call to 'print'

[limengfdu]

Dear all, I run the code "snippy --outdir 'SJ_2016_1531' --R1 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R1.fastq.gz' --R2 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R2.fastq.gz' --ref /home/edwin/template/bwa/tb_h37rv.fasta --cpus 16", it showed "Error running command, check SJ_2016_1531/snps.log".

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... 0.07 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 2.28 seconds elapse. [bwa_index] Update BWT... 0.07 sec [bwa_index] Pack forward-only FASTA... 0.05 sec [bwa_index] Construct SA from BWT and Occ... 0.88 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index reference/ref.fa [main] Real time: 3.367 sec; CPU: 3.352 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 16 reference/ref.fa /home/ND140/lm/cgMLST_test/SJ_2016_1531_R1.fastq.gz /home/ND140/lm/cgMLST_test/SJ_2016_1531_R2.fastq.gz | samtools view -@ 16 -F 3844 -q 60 -S -b -u -T reference/ref.fa - | samtools sort -o snps.bam -@ 16 -)

[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 70080 > reference/ref.txt

File "/home/lm/miniconda3/bin/fasta_generate_regions.py", line 7 print "usage: ", sys.argv[0], " " ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("usage: ", sys.argv[0], " ")?

Someone can help me solve the problem?