Snippy core.aln error 255


#1

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


#2

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


#3

Did you check these logs?


#4

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>”)?


#5

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>”)?


#6

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


#7

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


#8

Change the first line of

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

to read:

#!/usr/bin/env python2

and then restart nullarbor.


#9

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?


#10

Yes - you have miniconda3 installed and on your PATH:

Please follow the instructions in:

to mitigate this error.


#11

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