Closed ggabernet closed 4 years ago
I'll look at it right away.
Hi Maxime, sorry my bad. The convertAlleleCounts
process failed and that is why ASCAT was not triggered
so that's not the issue
OK, good to know, any idea what the problem was?
Fatal error: cannot open file '/home/ec2-user/.nextflow/assets/ggabernet/nf-core-sarek/bin/convertAlleleCounts.r': No such file or directory
I had to make a fork to fix the SamToFastq issue, but all the rest of the code is the same as the 2.5.2
release
Did it worked before? Or do you think that it was already an issue? Maybe we shouldn't use that to call the R script:
Rscript ${workflow.projectDir}/bin/convertAlleleCounts.r ...
yes that could be the issue, shouldn't it work directly with convertAlleleCounts.r
as the bin is added to the path?
I can test it out and let you know
I'll try it out on our cluster as well.
By the way, if you're using ASCAT, the current dev
has some good improvement.
You can now specify purity an ploidy
I've tried Rscript convertAlleleCounts.r
and directly convertAlleleCounts.r
(as you have the shebang Rscript line. Nothing works:
.command.sh: //nextflow-bin/convertAlleleCounts.r: /bin/env: bad interpreter: No such file or directory
It's a bit weird as it worked for me in Bcellmagic like the last option
Ah I just saw the shebang line was missing /usr/
, I try with this now
it also seems that there's a typo in the shebang for run_ascat.R as well
yes, I fixed both now, let's see
You're trying on AWS?
yes, I have to set it up there so we can run ASCAT on ICGC data
looks good now, the job was immediately killed before. But to make sure I'll post it when it runs through
Good, I made the same changes, and I'm trying it out on our server. You can make a PR, and if it works for everyone we can merge
perfect, will do!
This is solved now, but I am having another issue with ASCAT
, this time I switched already to the dev
branch as suggested:
[1] Reading Tumor LogR data...
[1] Reading Tumor BAF data...
[1] Reading Germline LogR data...
[1] Reading Germline BAF data...
[1] Registering SNP locations...
[1] Splitting genome in distinct chunks...
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [1]
Calls: ascat.GCcorrect -> colnames<-
In addition: Warning message:
In read.table(file = GCcontentfile, header = TRUE, as.is = TRUE) :
incomplete final line found by readTableHeader on 'input.5'
Execution halted
I love that R does not print the line number in errors...
skipping ascat.GCcorrect
works, there must be a problem in the GCcontentfile, but it's super hard to debug on AWS, will try on the cluster tomorrow
No problem executing R as we planned. But I had an issue with the GC file that wasn't recognized. I'll try to fix that.
OK, I found why you're having currently this bug with #127
I made a mistake with #107 and forgot to snake case fully the params for the ascat gc file in conf/igenomes.config
.
Since you already have a PR open open, I'll let you correct ac_lociGC
to ac_loci_gc
.
great, let's hope this solves the issues
Hi, when running Sarek with multiple variant callers, it seems like the first one is picked and the rest are ignored. I run it indicating Strelka and ASCAT, and ASCAT was just ignored.