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    MaxUlysse closed #814
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silviamorins
@silviamorins
ok, so if my sample is not multiplexed on several lanes, I should substitute the 1s with sample_1?
Maxime Garcia
@MaxUlysse
for example
If you do that, then it should work more smoothly
silviamorins
@silviamorins
Ok, thanks a lot for the time!
Maxime Garcia
@MaxUlysse
no problem
I assume you're working with WES
Maxime Garcia
@MaxUlysse
I'll try to add HsMetrics soonish
that would be an interesting QC
silviamorins
@silviamorins
yes exactly, those are the data
Maxime Garcia
@MaxUlysse
I'll put it on the top of my list ;-)
welchwilmerck
@welchwilmerck
I have validated nextflow with AWS Batch as well as https://github.com/SciLifeLab/Sarek/blob/master/docs/TESTS.md locally on an AWS instance. Now, I want to combine the two and run your tests on AWS Batch. After selecting the awsbatch profile and setting the queue and the bucket, I get:
Invalid AWS Batch job definition -- provide a Docker image name or a Batch job definition name
NF version 19.01
KochTobi
@KochTobi
What Sarek version are you using?
welchwilmerck
@welchwilmerck
commit a4ed8f34dcd6f9d0658f92c38fd53bc07ae5bc7c (HEAD -> master, tag: 2.3.FIX1, origin/master, origin/HEAD)
Merge: 7f7f2c2 8ca0194
Author: Maxime Garcia <max.u.garcia@gmail.com>
Date:   Mon Mar 4 10:56:09 2019 +0100
Maxime Garcia
@MaxUlysse
ok, so you should have docker image linked to it already without any issue
welchwilmerck
@welchwilmerck
I discovered that it works if I explicitly invoke the docker profile. Just awsbatch isn't enough. So, this is a nextflow configuration question. What's the difference between -profile awsbatch and -profile awsbatch,docker when both include conf/docker.config?
$ grep -8 docker nextflow.config
}

profiles {
  // AWS Batch with Docker profile
  // Docker images will be pulled automatically
  awsbatch {
    includeConfig 'conf/base.config'
    includeConfig 'conf/aws-batch.config'
    includeConfig 'conf/docker.config'
    includeConfig 'conf/igenomes.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/containers.config'
  }
  // Default config for german BinAC cluster
  // Runs the pipeline using the pbs executor
  // Singularity images will be pulled automatically
  binac {
--
    includeConfig 'conf/cfc.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/singularity.config'
    includeConfig 'conf/resources.config'
    includeConfig 'conf/containers.config'
  }
  // Small testing with Docker profile
  // Docker images will be pulled automatically
  docker {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/genomes.config'
    includeConfig 'conf/docker.config'
    includeConfig 'conf/containers.config'
  }
  // Small testing with Singularity profile
  // Singularity images will be pulled automatically
  singularity {
    includeConfig 'conf/base.config'
    includeConfig 'conf/travis.config'
    includeConfig 'conf/genomes.config'
Maxime Garcia
@MaxUlysse
@welchwilmerck That's quite a strange behavior, we always manage to make aws work with the aws profile
I'll make a PR, to remove travis configuration from docker, so that it'll be easier to mix profile
KochTobi
@KochTobi
worked for me with only providing the awsbatch profile. Maybe something to do with the genomes.config vs. igenomes.config on your side?
Szilveszter Juhos
@szilvajuhos
@MaxUlysse Looks my Mutect2 stuff works with the conda container, but tests are not - can/shall I help in finishing the conda configs? SciLifeLab/Sarek#789
silviamorins
@silviamorins

Hi, I am running nextflow run scilifelab/sarek/somaticVC.nf -r dev with --tools strelka,mutect2; I get the following:

Error report: Error executing process > 'ConcatVCF (MuTect2_[...]_Tumor_vs_[...]_Blood)'

Caused by:
  Process `ConcatVCF (MuTect2_[...]_Tumor_vs_[...]_Blood)` terminated with an error exit status (141)

Command executed:

  concatenateVCFs.sh -i human_g1k_v37_decoy.fasta.fai -c 10 -o MuTect2_[...]_Tumor_vs_[...]_Blood.vcf

Command exit status:
  141

Command output:
  (empty)

both .command.err and .command.log are empty.

Any ideas? If it's easier if I just report an issue let me know.
Thanks in advance!

Maxime Garcia
@MaxUlysse
Would be a good idea to make an issue, but it's quite strange that the .command.err .command.log are empty
Can you provide your .nextflow.log
silviamorins
@silviamorins
Rather not, sorry, as it contains private internal filenames... I can provide information, though, if you tell me what you're looking for
Maxime Garcia
@MaxUlysse
of course
I have no idea what I'm looking for in fact ;-)
silviamorins
@silviamorins
it ends with the same description of the error command reported above
Maxime Garcia
@MaxUlysse
I see
Maxime Garcia
@MaxUlysse
Quick question, how many vcf files are in the work folder waiting to be merged?
silviamorins
@silviamorins
(update: problem solved :) )
silviamorins
@silviamorins
Hi! Is there a reason why I can't specify the mice genome --genome 'GRCm38' in the runMain.sh? It only accepts versions from the human genome?
Maxime Garcia
@MaxUlysse
Hi, @silviamorins which version are you using?
silviamorins
@silviamorins
i.e., can I run Sarek on mice data and how should I provide the reference?
N E X T F L O W ~ version 19.01.0 Launching `scilifelab/sarek` - revision: a4ed8f34dc [2.3.FIX1]
Maxime Garcia
@MaxUlysse
OK, so basically, you would need to add GRCm38 in the genomes.config file
with the path to the ref files
silviamorins
@silviamorins
I feared that ...
Maxime Garcia
@MaxUlysse
You can help yourself with what Malin has done
silviamorins
@silviamorins
ok, thanks!
Maxime Garcia
@MaxUlysse
I'm currently porting sarek to nf-core, and working on that
but for the moment, I still need to test some stuff
silviamorins
@silviamorins
that's already great help, thanks
Maxime Garcia
@MaxUlysse
Glad that helped you
silviamorins
@silviamorins
Hi Maxime,
I am really struggling getting files that work for the mouse, and I know Malin is out of office now. I have downloaded the data from the Sanger institute now, and I keep getting as error A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig CHR_MG117_PATCH given as location, but this contig isn't present in the Fasta sequence dictionary. In the vcf files I see the no contigs assigned to unknown region of the chromosomes together with the "known" chromosomes, while in the fasta file those contigs are there, which is weird since these references come from the same database... I tried removing them from the fasta-related files, but still the error is there. Do qou have any other idea how I could deal with this? data was taken from ftp://ftp-mouse.sanger.ac.uk/.
Maxime Garcia
@MaxUlysse
Hi, sorry, I haven't replied earlier, I was on holiday as well, and going back again soon but just for a week, I'll try to help out as much as possible today, but I can't promise anything
silviamorins
@silviamorins
No worries and thanks!
silviamorins
@silviamorins
Update: I was using a .bed file from Ensembl, since there was no such file available from the Sanger institute, and there the contigs had different names compared to the files downloaded from Sanger. I am trying with a simple .bed derived from my fasta.fai now. So it was nothing pipeline-related, sorry! I hope this did not waste too much time.
Maxime Garcia
@MaxUlysse
No problem at all, I'm sorry I wasn't helpful at all
silviamorins
@silviamorins
No worries, as said it had nothing to do with Sarek!
Maxime Garcia
@MaxUlysse
Hi all, we'll be moving to https://nfcore.slack.com/channels/sarek