mpx:vadr (QC metrics) error

[DrB-S]

The last error I am seeing with Cecret is that vadr is terminating:

[e4/abdf4a] NOTE: Process mpx:vadr (QC metrics) terminated with an error exit status (255) -- Error is ignored

[erinyoung]

What vadr params are you using?

[DrB-S]

//# For process vadr //#NEW VADR options for monkeypox (see: https://github.com/ncbi/vadr/wiki/Monkeypox-virus-annotation ): //#Changed cpu number from 4 to 20 //## This one may be the correct one: params.vadr_options = '--split --glsearch -s -r --nomisc --r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin' params.vadr_reference = 'mpxv' params.vadr_trim_options = '--minlen 50 --maxlen 210000' params.vadr = true

[erinyoung]

These are the vadr-related params that I use with staphb's vadr container:

params.vadr = true
params.vadr_mdir = '/opt/vadr/vadr-models'
params.vadr_options = '--split --glsearch -s -r --nomisc --r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin'
params.vadr_reference  = 'mpxv'
params.vadr_trim_options  = '--minlen 50 --maxlen 210000'

Which ... look exactly the same as yours...

If you allowed the workflow to fail when vadr fails, what is the error message?

[DrB-S]

How do I allow the workflow to fail?

[DrB-S]

Do I take out errorStrategy = 'ignore' in the config? withName:vadr{ container = 'staphb/vadr:latest' errorStrategy = 'ignore' cpus = 20 }

[erinyoung]

Yes!

It's set to ignore vadr's errors by default because it fails when sequences are too short

[DrB-S]

Testing it now

[DrB-S]

monkeypox_vadr_failure.txt

[erinyoung]

What are in the log (/data/Sequence_analysis/Cecret/Analyses/monkeypox/10_genomes/work/7e/48a4ad5a1066c61fd5886e534c7e9b/logs/mpx:vadr/mpx:vadr.5b06a982-cebd-436b-8e73-e4af7b423b03.log) and error (/data/Sequence_analysis/Cecret/Analyses/monkeypox/10_genomes/work/7e/48a4ad5a1066c61fd5886e534c7e9b/logs/mpx:vadr/mpx:vadr.5b06a982-cebd-436b-8e73-e4af7b423b03.err) files?

[DrB-S]

See attached: mpx:vadr.5b06a982-cebd-436b-8e73-e4af7b423b03.log

[erinyoung]

It looks like it's printing out the help message. What is in the err file?

[DrB-S]

Tue Aug 9 18:15:25 MST 2022 Unknown option: r_lowsimok Unknown option: r_lowsimxd Unknown option: r_lowsimxl ERROR, unrecognized option; at /opt/vadr/vadr/v-annotate.pl line 590.

[erinyoung]

I know that error! You probably have to re-download your vadr container. When 1.4.2 got updated, the tag stayed the same. If you remove your old vadr container (either singularity or docker) and rerun the workflow, does that fix the issue?

[DrB-S]

Where is the vadr container?

[erinyoung]

Do you use singularity or docker?

To remove a docker container

docker rm vadr:1.4.2

To remove a singularity container, you have to delete the staphb-vadr-1.4.2.img file in wherever you're keeping your singularity files. The default is work/singularity of your launch directory, but you could have it set to a different place with a cacheDir variable.

[DrB-S]

Thanks. It was in nextflow_cachedir.

[DrB-S]

That solved it!! Works great!

[erinyoung]

Huzzah!!! I'm glad it was resolved.

[DrB-S]

Thanks again! Now on to resolving ‘ref_in_coord’ issue:-) It is showing up in lots of files.

Stephen M. Beckstrom-Sternberg, PhD Bioinformatics Contractor

Arizona State Public Health Lab Arizona Department of Health Services Cell: (602) 653-5011 Email: @.***

On Aug 11, 2022, at 3:17 PM, Young @.***> wrote:

Huzzah!!! I'm glad it was resolved.

— Reply to this email directly, view it on GitHub https://github.com/UPHL-BioNGS/Cecret/issues/115#issuecomment-1212552243, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVTVLJTDMWDMEVSNHISDD5DVYV3YDANCNFSM55XT5PXQ. You are receiving this because you modified the open/close state.

-- CONFIDENTIALITY NOTICE:  This e-mail is the property of the Arizona Department of Health Services and contains information that may be PRIVILEGED, CONFIDENTIAL, or otherwise exempt from disclosure by applicable law.  It is intended only for the person(s) to whom it is addressed.  If you have received this communication in error, please do not retain or distribute it.  Please notify the sender immediately by e-mail at the address shown above and delete the original message.  Thank you.  

grep 'ref_in_coord' / dataset/reference.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates iqtree2/iqtree2.iqtree:NOTE: Tree is UNROOTED although outgroup taxon 'ref_in_coord' is drawn at root iqtree2/iqtree2.iqtree:+-----------------------------------------------------------ref_in_coord iqtree2/iqtree2.iqtree:(ref_in_coord:0.0017018305,((Consensus_ERR3485802.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_ERR3485801.consensus_threshold_0.6_quality_20:0.0000005071):0.0000384397,(((Consensus_ERR3485797.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_ERR3485799.consensus_threshold_0.6_quality_20:0.0000005071):0.0000005071,Consensus_ERR3485800.consensus_threshold_0.6_quality_20:0.0000005071):0.0000005071,Consensus_ERR3485798.consensus_threshold_0.6_quality_20:0.0000005071):0.0000537884):0.0008604210,(MPXV-UK_P3_completeGenome:0.0000005071,(Consensus_SRR19536729.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_SRR19536728.consensus_threshold_0.6_quality_20:0.0000005071):0.0002536239):0.0011492286); iqtree2/iqtree2.log: 1 ref_in_coord 0.00% passed 91.12% iqtree2/iqtree2.mldist:ref_in_coord 0.00000000 0.00732890 0.00309139 0.00310965 0.00282096 0.00281075 0.00279419 0.00281164 0.00338687 0.00338675 iqtree2/iqtree2.treefile:(ref_in_coord:0.0017018305,((Consensus_ERR3485802.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_ERR3485801.consensus_threshold_0.6_quality_20:0.0000005071):0.0000384397,(((Consensus_ERR3485797.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_ERR3485799.consensus_threshold_0.6_quality_20:0.0000005071):0.0000005071,Consensus_ERR3485800.consensus_threshold_0.6_quality_20:0.0000005071):0.0000005071,Consensus_ERR3485798.consensus_threshold_0.6_quality_20:0.0000005071):0.0000537884):0.0008604210,(MPXV-UK_P3_completeGenome:0.0000005071,(Consensus_SRR19536729.consensus_threshold_0.6_quality_20:0.0000005071,Consensus_SRR19536728.consensus_threshold_0.6_quality_20:0.0000005071):0.0002536239):0.0011492286); grep: logs/cecret:fastp: Is a directory grep: logs/cecret:filter: Is a directory grep: logs/cecret:ivar: Is a directory grep: logs/cecret:markdup: Is a directory grep: logs/cecret:minimap2: Is a directory grep: logs/combine_results: Is a directory grep: logs/mpx:nextclade: Is a directory grep: logs/mpx:vadr: Is a directory grep: logs/msa:iqtree2: Is a directory grep: logs/msa:nextalign: Is a directory grep: logs/msa:snpdists: Is a directory grep: logs/multiqc_combine: Is a directory grep: logs/qc:bcftools_variants: Is a directory grep: logs/qc:fastqc: Is a directory grep: logs/qc:ivar_variants: Is a directory grep: logs/qc:kraken2: Is a directory grep: logs/qc:samtools_coverage: Is a directory grep: logs/qc:samtools_depth: Is a directory grep: logs/qc:samtools_flagstat: Is a directory grep: logs/qc:samtools_intial_stats: Is a directory grep: logs/qc:samtools_stats: Is a directory grep: logs/summary: Is a directory grep: multiqc/multiqc_data: Is a directory nextalign/nextalign.aligned.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG001.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG002.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG003.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG005.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG015.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG019.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG021.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG022.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG023.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG024.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG025.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG027.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG029.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG030.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG031.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG034.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG035.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG036.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG037.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG038.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG039.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG040.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG042.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG043.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG044.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG045.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG046.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG047.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG048.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG049.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG050.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG051.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG052.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG053.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG054.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG055.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG056.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG057.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG058.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG059.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG060.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG061.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG062.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG063.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG064.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG065.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG066.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG068.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG069.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG070.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG071.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG072.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG074.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG075.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG076.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG077.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG078.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG079.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG080.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG081.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG082.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG083.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG084.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG085.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG086.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG087.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG088.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG089.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG090.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG091.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG092.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG093.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG094.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG095.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG096.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG097.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG098.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG099.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG100.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG101.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG102.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG103.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG104.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG105.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG106.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG107.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG108.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG109.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG110.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG111.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG112.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG113.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG114.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG115.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG116.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG117.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG118.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG119.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG120.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG121.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG122.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG123.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG124.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG125.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG126.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG127.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG128.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG129.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG130.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG131.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG132.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG133.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG134.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG135.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG136.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG137.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG138.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG139.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG140.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG141.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG142.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG143.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG144.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG145.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG146.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG147.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG148.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG149.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG150.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG151.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG153.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG154.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG155.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG156.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG157.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG158.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG159.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG160.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG161.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG162.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG163.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG164.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG165.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG167.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG170.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG171.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG172.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG173.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG174.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG175.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG176.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG178.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG180.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG181.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG185.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG187.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG188.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG189.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG190.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG191.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG192.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG193.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG195.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG197.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG198.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG199.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG200.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG204.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG205.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG208.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG209.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates nextalign/nextalign_gene_OPG210.translation.fasta:>ref_in_coord Reference sequence in coord.fasta coordinates snp-dists/snp-dists.txt:snp-dists 0.8.2,ref_in_coord,Consensus_ERR3485802.consensus_threshold_0.6_quality_20,Consensus_ERR3485797.consensus_threshold_0.6_quality_20,MPXV-UK_P3_completeGenome,Consensus_ERR3485799.consensus_threshold_0.6_quality_20,Consensus_ERR3485798.consensus_threshold_0.6_quality_20,Consensus_ERR3485801.consensus_threshold_0.6_quality_20,Consensus_ERR3485800.consensus_threshold_0.6_quality_20,Consensus_SRR19536729.consensus_threshold_0.6_quality_20,Consensus_SRR19536728.consensus_threshold_0.6_quality_20 snp-dists/snp-dists.txt:ref_in_coord,0,102,166,560,505,504,501,504,610,610

logs/msa:iqtree2/msa:iqtree2.168b70e4-d7a6-48bf-86a6-5d7b2ce294bb.log: 1 ref_in_coord 0.00% passed 91.12%

grep ref_in_coord work/////* work/e5/2f5803af32e973ef6c53ea704b5de9/logs/msa:iqtree2/msa:iqtree2.168b70e4-d7a6-48bf-86a6-5d7b2ce294bb.log: 1 ref_in_coord 0.00% passed 91.12%