Scaffolds output tigmint-arcs error

[JordideRaad]

Dear Shaun and Lauren,

Thanks to your advice concerning the tigmint-cut update, I was able to make tigmint work and locate possible mis-assemblies in my scaffold file. However, when trying to re-scaffold my broken assembly with tigmint arcs, I get and error message when the program is trying to write the final scaffold file:

stderr_arcs.txt

Nevertheless, the run output seems fine:

stdout_arcs.txt

Any idea what might have caused this error? I cant seem to figure it out.

It might be that this is related to the dependency of Links, as brew install links-scaffolder was not available, and I had to install the related dependencies of ARCS individually (https://github.com/bcgsc/arcs)

brew.txt

Any advice is highly appreciated.

Kind regards,

Jordi de Raad

[lcoombe]

Hi Jordi,

First, the warning about unpaired reads is indicating that there are reads in your alignment file (of barcoded reads to the post-Tigmint scaffolds) that are not paired (ARCS requires that read pairs should be consecutive in the BAM file). Is your input linked reads file interleaved? Did you get a non-empty output *.arcs_original.gv file? If so, then it indicates that ARCS skipped some of the read alignments, but still was able to construct a scaffold graph OK.

The final error is a bit strange, because it appears that LINKS completed successfully, but the Makefile indicates that there was an error:

make: *** [N15Minsize50000.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.c5_e30000_r0.05.arcs.a0.1_l10.links.scaffolds.fa] Error 255
make: *** Deleting file `N15Minsize50000.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.c5_e30000_r0.05.arcs.a0.1_l10.links.scaffolds.fa'

Can you confirm that the "links.scaffolds.fa" file was deleted by the Makefile? Also, could you show us a couple of lines of the "links.scaffolds" file -- this basically lists all the headers of the output file, so might indicate if successful joins were still make by LINKS.

Thanks! Lauren

[lcoombe]

Also - Just so you know, I'm out of the office from this afternoon to the end of the week, but hopefully @sjackman will have time to help you troubleshoot!

[sjackman]

Error: No available formula with the name "links-scaffolder"

Thanks for the bug report, Jordie. I've update the installation instructions. https://github.com/bcgsc/tigmint#install-the-dependencies-of-arcs-optional

brew tap brewsci/bio
brew tap brewsci/science
brew install arcs links-scaffolder

[sjackman]

/home/jderaad/softwares/conda/anaconda3/envs/tigmint/bin/LINKS [v1.8.4] terminated successfully on Mo 28. Mai 22:46:11 CEST 2018
make: *** [N15Minsize50000.barcoded.as0.65.nm5.molecule.size2000.trim0.window1000.span20.breaktigs.barcoded.c5_e30000_r0.05.arcs.a0.1_l10.links.scaffolds.fa] Error 255

I see that you're running LINKS 1.8.4, and that's also the most recent version in Brewsci/science. LINKS had a bug wherein it would return failure (exit status 255) even though it had in fact succeeded, which caused make to believe that LINKS had failed. I'll package LINKS 1.8.6 for Brewsci/bio. In the mean time, you could install LINKS 1.8.6 manually from https://github.com/bcgsc/LINKS/releases

[sjackman]

LINKS 1.8.5 is now in Brewsci/bio, which should resolve this issue.

brew update
brew tap brewsci/bio
brew upgrade links-scaffolder

Thanks again for the bug report, @JordideRaad !

[JordideRaad]

Dear Shaun and Lauren,

Thank you again for the amazing support so far. Indeed, removing the old version of links (1.8.4) and installing the dependency as Shaun mentioned works now.

I only got one slight error at the final step, stating that the gsed command was not found. I could easily fix this with brew install gnu-sed.

Thanks again for all the support!

Kind regards,

Jordi

[sjackman]

I've committed https://github.com/bcgsc/tigmint/commit/b98bf28ce72a06cffcfe47dfab0c2dd6bf088542 just now to fix the gsed issue. It will be included with the next stable release of Tigmint. Thanks for the bug report!