Please add seqtk among the packages to install in env/mtoolbox.yaml

Thanks
C

GSNAP 2020 version does not work properly when building genome indexes, while GSNAP 2018 works fine. Mabe downgrade current GSNAP version to 2018. We should discuss @domenico-simone

Does this version support unpaired fastq reads as well? @domenico-simone

Working with

commit 522b9d4cf59e5e71275dbca08a047bdf2d9cbaab (HEAD, origin/new_alignment_wf_3, new_alignment_wf_3)

error raised on line 62 of this snakefile: https://github.com/mitoNGS/MToolBox_snakemake/blob/master/snakefiles/variant_calling.snakefile

when dealing with sample names in analysis.tab file, because integers cannot be subjected to re.escape(x) function

Hi, thank you for this convenient tool.

I'd like to call variants using human mtDNA. In the reference_genomes.tab, we need to specify ref_genome_mt and ref_genome_n.

I'd like to use hg19 as a reference. I downloaded genome data of hg19, but this genome data include chrM(and chrMT).
Should I remove mtDNA sequence from hg19 genome date when I use hg19 as ref_genome_n?
then Should I speficy rCRS fasta data for ref_genome_mt?

best regards,

I often get this error when the first run fails and have to rerun the analysis. This occurs when I run MToolBox as:

MToolBox-variant-calling -rpk -j 5 --cluster-config cluster.yaml --latency-wait 60 --cluster 'sbatch -p cluster7 -n {cluster.threads} -t {cluster.time} -o {cluster.stdout}'

This is the error:
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:

If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

We've migrated to an air-gap system with no outgoing internet connection and I can no longer get MToolBox to work.

I filed an issue a month ago but haven't heard anything back (mitoNGS/MToolBox#96) so I'm trying to get a container solution working.

However, I need some help getting this to run: https://hub.docker.com/r/mitongs/mtoolbox

It's not clear to me how I can edit/provide-symlinks for analysis.tab, datasets.tab, reference_genomes.tab and provide the datasets to the container.

Question 1:

Can you please help show me how the syntax would look like for that?

Question 2:

I'm able to activate the mtoolbox conda environment from the Docker container:

$ sudo docker run -it mitongs/mtoolbox:latest
 :: MToolBox ::  / >>> source activate mtoolbox
(mtoolbox)  :: MToolBox ::  / >>> 

However, I'm not able to do so from the Singularity container?
Can you spot what I'm doing wrong?

$ sudo singularity build --sandbox mtoolbox.sif docker://mitongs/mtoolbox:latest
$ singularity run mtoolbox.sif 
Singularity> source activate mtoolbox
Could not find conda environment: mtoolbox
You can list all discoverable environments with `conda info --envs`.

I seem to be having an error compiling the .sh file.
Thanks.

Please merge U1 and U2 into the same file.

Please add a second switch to skip U orphans at the first mapping step.

Thanks
C

Thanks!

In this scenario, vcf files should just be copied in results.

return an empty VCF and a better error message

When keep_orphans=True, too many files are provided to gsnap. Possible workaround: cat all SE files in one.