Nullarbor report without reads

[cmkobel]

Hello.

We have become very excited about Nullarbor, and especially the report.

I wondered if it would be somehow possible to the isolate set part of the pipeline. That is, without reads and subsequent assembly?

It seems that this is not supported - But would it be possible to somehow edit the makefile, so that it only computes the set analysis, and prints the report?

Kind regards

[tseemann]

The capability to begin with assemblies instead of reads (or mix thereof) is an existing open issue.

It might be possible to hack it to work. You would need to pre-create the ID/contigs.fa files from your assemblies, or do this automatically using --prefill and [prefill] in nullarbor.conf but also make some fake reads.

If you have assemblies only, maybe just upload them into https://pathogen.watch ?

[mabouelk]

Hi @tseemann I finally installed Nullarbor on my mac and achieved the medal for that part. But when I run it on the reads, the run stop after 20 minutes and I found that only one isolate get assembled but not the remaining 17 ones. Here is the error for that: make: [Makefile:80: ref.fa] Error 1 make: Deleting file 'ref.fa' make: *** Waiting for unfinished jobs and at the end I got this DONE make: Leaving directory '/Users/moh/TRY'

I found that I can use prefill for assembled contigs so I used shovill to assemble all of the isolates separately and then used prefill but I got this error: [14:49:30] Pre-filling 'kraken.tab' from /home/seq/MDU/QC/{ID}/kraken2.tab [14:49:30] Pre-filled 0 'kraken.tab' files (22 missing) [14:49:30] Pre-filling 'prokka.gff' from /home/seq/MDU/QC/{ID}/prokka.gff [14:49:30] Pre-filled 0 'prokka.gff' files (22 missing) [14:49:30] Pre-filling 'yield.tab' from /home/seq/MDU/QC/{ID}/yield.tab [14:49:30] Pre-filled 0 'yield.tab' files (22 missing) and what is the right command for Nullarbor with prefill as mine was that: nullarbor.pl --name SPSE --mlst spseudintermedius --ref Downloads/rawseq_3_26_2020/06-3228.gbk --input Downloads/rawseq_3_26_2020/input.txt --outdir OUTDIR3

[mabouelk]

even running make preview I got this:

Writing to Isolate12/sketch.msh... mash paste preview Isolate4/sketch.msh Isolate17/sketch.msh Isolate21/sketch.msh Isolate16/sketch.msh Isolate18/sketch.msh Isolate6/sketch.msh Isolate7/sketch.msh Isolate11/sketch.msh Isolate22/sketch.msh Isolate1/sketch.msh Isolate15/sketch.msh Isolate8/sketch.msh Isolate14/sketch.msh Isolate5/sketch.msh Isolate20/sketch.msh Isolate2/sketch.msh Isolate19/sketch.msh Isolate9/sketch.msh Isolate13/sketch.msh Isolate3/sketch.msh Isolate10/sketch.msh Isolate12/sketch.msh Writing preview.msh... cat isolates.txt | wc -l > preview.mat mash dist -p 4 -t preview.msh preview.msh | grep -v '^#' | sed 's/\/R1.fq.gz//' >> preview.mat quicktree -in m -out t preview.mat | nw_order -c n - > preview.nwk nw_display -S -s -w 1024 -l 'font-size:12;font-family:sans-serif;' -i 'opacity:0' -b 'opacity:0' -v 16 preview.nwk > preview.svg fq --ref ref.fa Isolate4/R1.fq.gz Isolate4/R2.fq.gz > Isolate4/yield.tab [fq] running command: cat Isolate4/R1.fq.gz Isolate4/R2.fq.gz | seqtk fqchk -q0 - [fq] processed 11462686 reads. [fq] calculating depth, using size (via --ref ref.fa) Illegal division by zero at /Users/moh/miniconda3/envs/nullarobr_env/bin/fq line 67, <$IN> line 153. make: [Makefile:136: Isolate4/yield.tab] Error 2 make: Deleting file 'Isolate4/yield.tab'