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bcgsc / tigmint

⛓ Correct misassemblies using linked AND long reads
https://bcgsc.github.io/tigmint/
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Error when attempting tigmint-make arcs #50

Closed katherinedougan closed 3 years ago

katherinedougan commented 3 years ago

I have already completed running Tigmint on my assembly, but now I would like to add on the scaffolding with ARCS and to run metrics. However, when I run it with the -n flag first to make sure it won't overwrite any files, I get the error below. I previously got a similar error in the beginning when first attempting to run tigmint. However, I realized it was due to an error with a file name so that has already been corrected so I'm not sure what the issue is now. Below are the input file names, my command, and the resulting error.

Input files Dtrenchii_assembly_v2.CCMP2556_10xreads_longranger.sortbx.bam Dtrenchii_assembly_v2.fa

Command tigmint-make metrics draft=Dtrenchii_assembly_v2 reads=CCMP2556_10xreads_longranger -n

Output abyss-fac -G-1 -t500 Dtrenchii_assembly_v2.fa >Dtrenchii_assembly_v2.abyss-fac.tsv seqtk seq Dtrenchii_assemblyv2.fa | tr '~' | abyss-fatoagp -f Dtrenchii_assembly_v2.scaftigs.fa >Dtrenchii_assembly_v2.scaftigs.fa.agp abyss-fac -G-1 -t500 Dtrenchii_assembly_v2.scaftigs.fa >Dtrenchii_assembly_v2.scaftigs.abyss-fac.tsv make: *** No rule to make target 'Dtrenchii_assembly_v2.scaftigs.ref.samtobreak.tsv', needed by 'draft_metrics'. Stop.

lcoombe commented 3 years ago

Hi @kedougan,

It looks like you are missing the ref and G parameters for specifying the reference to use and the genome size. The reference would just be needed to run the full metrics (Not required for ARCS).

If you do not have a reference for this assembly work, then I'd recommend just running ARCS separately (With target arcs), and running abyss-fac for the reference-free stats. If you do have a reference, you can run your above command once you specify those parameters (https://github.com/bcgsc/tigmint#usage), but I'd recommend running QUAST for reference-based assembly quality metrics. When Tigmint was first developed, QUAST couldn't handle large genomes, but it does now. If it is of interest, we could put updating the metrics target to run QUAST on our TODO list.

Thank you for your interest in Tigmint! Lauren

github-actions[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had any recent activity. It will be closed if no further activity occurs. Thank you for your interest in Tigmint!