snippy/freebayes fail

[patmsim]

Hi,

I'm new to nullarbor but the pipeline seems great. I started a test (3 bacterial genomes in Illumina PE) to see if the installation was good (for the installation I used linuxbrew and folloed the link recommended on nullarbor github home page)

Everything goes smoothly until the snps analysis starts. Here is the terminal info and the snps.log info

snippy --cpus 4 --force --outdir Isolate1/Isolate1 --ref /home/pms/Desktop/test_nullabor/test_CC30/MN8_MSSA_ST30.gbk --R1 Isolate1/R1.fq.gz --R2 Isolate1/R2.fq.gz [10:49:17] This is snippy 3.1 [10:49:17] Written by Torsten Seemann torsten.seemann@gmail.com [10:49:17] Obtained from https://github.com/tseemann/snippy [10:49:17] Detected operating system: linux [10:49:17] Enabling bundled linux tools. [10:49:17] Found bwa - /home/pms/.linuxbrew/bin/bwa [10:49:17] Found samtools - /home/pms/.linuxbrew/bin/samtools [10:49:17] Found tabix - /home/pms/.linuxbrew/bin/tabix [10:49:17] Found bgzip - /home/pms/.linuxbrew/bin/bgzip [10:49:17] Found snpEff - /home/pms/.linuxbrew/Cellar/snippy/3.1/bin/../binaries/noarch/snpEff [10:49:17] Found java - /home/pms/.linuxbrew/bin/java [10:49:17] Found gzip - /bin/gzip [10:49:17] Found parallel - /home/pms/.linuxbrew/bin/parallel [10:49:17] Found freebayes - /home/pms/.linuxbrew/bin/freebayes [10:49:17] Found freebayes-parallel - /home/pms/.linuxbrew/bin/freebayes-parallel [10:49:17] Found fasta_generate_regions.py - /home/pms/.linuxbrew/bin/fasta_generate_regions.py [10:49:17] Found vcfstreamsort - /home/pms/.linuxbrew/bin/vcfstreamsort [10:49:17] Found vcfuniq - /home/pms/.linuxbrew/bin/vcfuniq [10:49:17] Found vcffirstheader - /home/pms/.linuxbrew/bin/vcffirstheader [10:49:17] Found vcf-consensus - /home/pms/.linuxbrew/bin/vcf-consensus [10:49:17] Found snippy-vcf_to_tab - /home/pms/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_to_tab [10:49:17] Found snippy-vcf_report - /home/pms/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_report [10:49:17] Found snippy-vcf_filter - /home/pms/.linuxbrew/Cellar/snippy/3.1/bin/snippy-vcf_filter [10:49:17] Using reference: /home/pms/Desktop/test_nullabor/test_CC30/MN8_MSSA_ST30.gbk [10:49:17] Treating reference as 'genbank' format. [10:49:17] Will use 4 CPU cores. [10:49:17] Using read file: /home/pms/Desktop/test_nullabor/test_CC30/results_CC30_AT/Isolate1/R1.fq.gz [10:49:17] Using read file: /home/pms/Desktop/test_nullabor/test_CC30/results_CC30_AT/Isolate1/R2.fq.gz [10:49:17] Deleting all files in existing folder: Isolate1/Isolate1 [10:49:17] Changing working directory: Isolate1/Isolate1 [10:49:17] Creating reference folder: reference [10:49:17] Extracting FASTA and GFF from reference. [10:49:18] Wrote 1 sequences to ref.fa [10:49:18] Wrote 2916 features to ref.gff [10:49:18] Creating reference/snpeff.config [10:49:18] Freebayes will process 16 chunks of 1000 bp, 4 chunks at a time. [10:49:18] Using BAM RG (Read Group) ID: snps [10:49:18] Running: samtools faidx reference/ref.fa 2>> snps.log [10:49:18] Running: bwa index reference/ref.fa 2>> snps.log [10:49:18] Error running command, check Isolate1/Isolate1/snps.log make: *** [Isolate1/Isolate1/snps.tab] Error 2 make: Leaving directory `/home/pms/Desktop/test_nullabor/test_CC30/results_CC30_AT'

Now the snps.log information:

samtools faidx reference/ref.fa

bwa index reference/ref.fa

[bwa_index] Pack FASTA... [bns_fasta2bntseq] Failed to allocate 0 bytes at bntseq.c line 303: Success

I am a newbie in programming and I am just starting to get used to shell.

Can you help me as to what is wrong and I should be fixing ??

Thank you.

[andersgs]

Hi. Can you confirm there is any sequence data in your reference Genbank file?

[patmsim]

Hi,

Thanks fro your return. Indeed the genbak didn't have the sequence ! I'm re-running nullarbor and I'll let you know if it works.

[patmsim]

Hi,

Yes it works !!:-) Small problem with Vcf.pm but i searched on the issues page of snippy and found the answer @ https://github.com/tseemann/snippy/issues/81

Thanks a lot for your help and for the great tools you have created !

[tseemann]

Glad you got it working @patmsim !