Snippy core.aln error 255

[Ebenn]

Hi Matt,
I am running nullarbor2, it has terminated with the error message below:

> snps.log

[16:25:30] Running: tabix -s 1 -b 2 -e 2 snps.depth.gz 2>> snps.log

[16:25:30] Running: fasta_generate_regions.py reference/ref.fa.fai 59503 > reference/ref.txt 2>> snps.log

[16:25:30] Error running command, check 17AE/snippy/snps.log

cp: cannot stat ‘17AE/snippy/snps.tab’: No such file or directory

cp: cannot stat ‘17AE/snippy/snps.aligned.fa’: No such file or directory

cp: cannot stat ‘17AE/snippy/snps.vcf’: No such file or directory

‘17AE/snippy/snps.bam’ -> ‘17AE/snps.bam’

‘17AE/snippy/snps.bam.bai’ -> ‘17AE/snps.bam.bai’

‘17AE/snippy/snps.log’ -> ‘17AE/snps.log’

snippy-core --ref ref.fa 17BD 17AB 17AF 17BE 17BG 4AD 17AC 17BF 49BB 19BD 17BA 07BC 17AA 17AE

[16:25:30] Loading Snippy folders

[16:25:30] Using ID ‘17BD’ for 17BD

[16:25:30] Could not find default 17BD/snps.tab, using 17BD/kraken.tab instead

[16:25:30] Unexpected header in 17BD/kraken.tab: 26.84 399665 399665 U 0

unclassified

Makefile:82: recipe for target ‘core.aln’ failed

make: *** [core.aln] Error 255

make: Leaving directory ‘/home/ubuntu/seq02/ebenn/gbs_nullarbor/gbs_nullarbor_run19Sep2018’

Any help, please?

Thx
Ebenn

[Ebenn]

I an experiencing a related error on a separate nullarbor run. Pls see below:

[10:58:11] Using BAM RG (Read Group) ID: snps

[10:58:11] Running: samtools faidx reference/ref.fa 2>> snps.log

[10:58:11] Running: bwa index reference/ref.fa 2>> snps.log

[10:58:14] Running: mkdir reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log

[10:58:14] Running: mkdir reference/ref && bgzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log

[10:58:14] Running: (bwa mem -v 2 -M -R ‘@RG\tID:snps\tSM:snps’ -t 4 reference/ref.fa /home/ubuntu/efn/seqrun_3/nullarbor/nullarbor_results/g_fowl_only_nullarbor_run17Sep2018/G-fowl4-1/R1.fq.gz /home/ubuntu/efn/seqrun_3/nullarbor/nullarbor_results/g_fowl_only_nullarbor_run17Sep2018/G-fowl4-1/R2.fq.gz | samtools view -u -T reference/ref.fa -F 3844 -q 60 | samtools sort --reference reference/ref.fa > snps.bam) 2>> snps.log

[10:59:45] Running: samtools index snps.bam 2>> snps.log

[10:59:45] Running: samtools depth -aa -q 20 snps.bam | bgzip > snps.depth.gz 2>> snps.log

[10:59:45] Running: tabix -s 1 -b 2 -e 2 snps.depth.gz 2>> snps.log

[10:59:45] Running: fasta_generate_regions.py reference/ref.fa.fai 127598 > reference/ref.txt 2>> snps.log

[10:59:45] Error running command, check G-fowl4-1/snippy/snps.log

cp: cannot stat ‘G-fowl4-1/snippy/snps.tab’: No such file or directory

cp: cannot stat ‘G-fowl4-1/snippy/snps.aligned.fa’: No such file or directory

cp: cannot stat ‘G-fowl4-1/snippy/snps.vcf’: No such file or directory

‘G-fowl4-1/snippy/snps.bam’ -> ‘G-fowl4-1/snps.bam’

‘G-fowl4-1/snippy/snps.bam.bai’ -> ‘G-fowl4-1/snps.bam.bai’

‘G-fowl4-1/snippy/snps.log’ -> ‘G-fowl4-1/snps.log’

snippy-core --ref ref.fa G-fowl9-2 G-fowl7-3 G-fowl1-1 G-fowl2-3 G-fowl5-2 G-fowl3-1 G-fowl3-2 G-fowl2-4 G-fowl6-3 G-fowl2-2 G-fowl6-2 G-fowl5-4 G-fowl9-1 G-fowl7-4 G-fowl4-5 G-fowl7-1 G-fowl3-3 G-fowl9-5 G-fowl1-4 G-fowl6-5 G-fowl7-5 G-fowl2-5 G-fowl1-5 G-fowl1-3 G-fowl6-4 G-fowl2-1 G-fowl9-4 G-fowl4-2 G-fowl5-1 G-fowl4-3 G-fowl1-2 G-fowl4-4 G-fowl9-3 G-fowl5-5 G-fowl6-1 G-fowl3-5 G-fowl3-4 G-fowl7-2 G-fowl5-3 G-fowl4-1

[10:59:46] Loading Snippy folders

[10:59:46] Using ID ‘G-fowl9-2’ for G-fowl9-2

[10:59:46] Could not find default G-fowl9-2/snps.tab, using G-fowl9-2/kraken.tab instead

[10:59:46] Unexpected header in G-fowl9-2/kraken.tab: 2.51 10484 10484 U 0 unclassified

Makefile:82: recipe for target ‘core.aln’ failed

make: *** [core.aln] Error 255

make: Leaving directory ‘/home/ubuntu/efn/seqrun_3/nullarbor/nullarbor_results/g_fowl_only_nullarbor_run17Sep2018’

Grateful for your help!
Ebenn

[mattbull]

[16:25:30] Error running command, check 17AE/snippy/snps.log

[10:59:45] Error running command, check G-fowl4-1/snippy/snps.log

Did you check these logs?

[Ebenn]

check G-fowl4-1/snippy/snps.log

The log for this one looks like this:

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -v 2 -M -R @RG\tID:snps\tSM:snps -t 4 reference/ref.fa /home/ubuntu/efn/seqrun_3/nullarbor/nullarbor_results/g_fowl_only_nullarbor_run17Sep2018/G-fowl4-1/R1.fq.gz /home/ubuntu/efn/seqrun_3/nullarbor/nullarbor_results/g_fowl_only_nullarbor_run17Sep2018/G-fowl4-1/R2.fq.gz

[main] Real time: 91.169 sec; CPU: 273.304 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 127598 > reference/ref.txt

File “/home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.py”, line 7

print "usage: “, sys.argv[0], " <fasta file or index file> <region size>”

^

SyntaxError: Missing parentheses in call to ‘print’. Did you mean print("usage: “, sys.argv[0], " <fasta file or index file> <region size>”)?

[Ebenn]

check 17AE/snippy/snps.log

Similar for this one too, pls:

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[M::mem_pestat] skip orientation FF as there are not enough pairs

[M::mem_pestat] skip orientation FR as there are not enough pairs

[M::mem_pestat] skip orientation RF as there are not enough pairs

[M::mem_pestat] skip orientation RR as there are not enough pairs

[main] Version: 0.7.17-r1188

[main] CMD: bwa mem -v 2 -M -R @RG\tID:snps\tSM:snps -t 4 reference/ref.fa /home/ubuntu/seq02/ebenn/gbs_nullarbor/gbs_nullarbor_run19Sep2018/17AE/R1.fq.gz /home/ubuntu/seq02/ebenn/gbs_nullarbor/gbs_nullarbor_run19Sep2018/17AE/R2.fq.gz

[main] Real time: 78.213 sec; CPU: 294.560 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 59503 > reference/ref.txt

File “/home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.py”, line 7

print "usage: “, sys.argv[0], " <fasta file or index file> <region size>”

^

SyntaxError: Missing parentheses in call to ‘print’. Did you mean print("usage: “, sys.argv[0], " <fasta file or index file> <region size>”)?

[mattbull]

Did you install miniconda? The problem is similar to the one you described in this thread:

Installing Nullarbor in python environment

The way that print function is called changed between Python 2 and 3. The error below is caused by trying to run a program written in Python 2 (fasta_generate_regions.py) using the Python 3 interpreter. I suspect that conda is still interfering with your environment. The default miniconda3 python interpreter is currently something like version 3.6.4, and the default Ubuntu 16.04 interpreter is something like version 2.7.12. If you used the automatic miniconda installer, it gives you the optio…

[Ebenn]

Hi Matt,
No, I did not install conda, nor am I working in a conda environment at the moment. What may I do to solve the problem, please? Is this because I am using nullarbor2 this time around?

Thx
Ebenn

[mattbull]

Change the first line of

/home/linuxbrew/.linuxbrew/bin/fasta_generate_regions.py

to read:

#!/usr/bin/env python2

and then restart nullarbor.

[Ebenn]

Thx Matt,
Have just done that and restarted nullarbor, but getting an error message about yaml::tiny module below:

nullarbor2.pl --name nhp_nullarbor --mlst ecoli --ref /home/ubuntu/efn/seqrun_3/nullarbor/E_coli_2348_69_ref.fasta --input nullarbor_nhp_input_files.tab --outdir nhp_nullarbor_run17Sep2018

Can’t locate YAML/Tiny.pm in @INC (you may need to install the YAML::Tiny module) (@INC contains: /home/ubuntu/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/site_perl/5.26.2 /home/ubuntu/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/5.26.2 .) at /home/linuxbrew/.linuxbrew/bin/nullarbor2.pl line 13.

BEGIN failed–compilation aborted at /home/linuxbrew/.linuxbrew/bin/nullarbor2.pl line 13.

Did I miss something, please?

[mattbull]

Yes - you have miniconda3 installed and on your PATH:

Can’t locate YAML/Tiny.pm in @INC (you may need to install the YAML::Tiny module) (@INC contains: /home/ubuntu/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/site_perl/5.26.2 /home/ubuntu/miniconda3/lib/5.26.2/x86_64-linux-thread-multi /home/ubuntu/miniconda3/lib/5.26.2 .) at /home/linuxbrew/.linuxbrew/bin/nullarbor2.pl line

Please follow the instructions in:

Installing Nullarbor in python environment

The way that print function is called changed between Python 2 and 3. The error below is caused by trying to run a program written in Python 2 (fasta_generate_regions.py) using the Python 3 interpreter. I suspect that conda is still interfering with your environment. The default miniconda3 python interpreter is currently something like version 3.6.4, and the default Ubuntu 16.04 interpreter is something like version 2.7.12. If you used the automatic miniconda installer, it gives you the optio…

to mitigate this error.