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caleblareau / mgatk

mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
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Error in .local(assays, ...) : unused argument (rowData = <S4 object of class "GRanges">) #31

Closed francat closed 3 years ago

francat commented 3 years ago

Hi Caleb,

I am trying to run the example provided for mgatk tenx under mgatk/tests and am running into some issues. I tried with the --skip-R and/or --snake-stdouts flag to my command but still end up with the same error. I'm running the program on a hpc. 

Thu Feb 11 17:20:19 PST 2021: Found bam file: barcode/test_barcode.bam for genotyping.
Thu Feb 11 17:20:19 PST 2021: Found file of barcodes to be parsed: barcode/test_barcodes.txt
Thu Feb 11 17:20:19 PST 2021: User specified mitochondrial genome matches .bam file
Thu Feb 11 17:20:24 PST 2021: Finished determining/splitting barcodes for genotyping.
Thu Feb 11 17:20:24 PST 2021: Genotyping samples with 2 threads
Error in .local(assays, ...) :
  unused argument (rowData = <S4 object of class "GRanges">)
Calls: importMito ... SummarizedExperiment -> SummarizedExperiment -> .local
Execution halted

Here is a list of files from the output directory

ls -lRh bc1dmem
.:

total 12K
4.0K drwxr-xr-x 2 fran_catalan ucb 4.0K Feb 11 22:36 final
4.0K drwxr-xr-x 4 fran_catalan ucb 4.0K Feb 11 17:20 logs
4.0K drwxr-xr-x 4 fran_catalan ucb 4.0K Feb 11 17:14 qc

./final:
total 648K
 96K -rw-r--r-- 1 fran_catalan ucb  96K Feb 11 22:36 bc1.A.txt.gz
100K -rw-r--r-- 1 fran_catalan ucb  96K Feb 11 22:36 bc1.C.txt.gz
 52K -rw-r--r-- 1 fran_catalan ucb  50K Feb 11 22:36 bc1.G.txt.gz
 80K -rw-r--r-- 1 fran_catalan ucb  77K Feb 11 22:36 bc1.T.txt.gz
196K -rw-r--r-- 1 fran_catalan ucb 194K Feb 11 22:36 bc1.coverage.txt.gz
4.0K -rw-r--r-- 1 fran_catalan ucb   76 Feb 11 22:36 bc1.depthTable.txt
120K -rw-r--r-- 1 fran_catalan ucb 119K Feb 11 22:35 chrM_refAllele.txt

./logs:
total 28K
4.0K -rw-r--r-- 1 fran_catalan ucb 1.1K Feb 11 22:36 base.mgatk.log
4.0K -rw-r--r-- 1 fran_catalan ucb  474 Feb 11 22:35 bc1.parameters.txt
4.0K -rw-r--r-- 1 fran_catalan ucb 3.0K Feb 11 22:36 bc1.snakemake_tenx.log
8.0K -rw-r--r-- 1 fran_catalan ucb 6.8K Feb 11 22:36 bc1.snakemake_tenx.stats
4.0K drwxr-xr-x 2 fran_catalan ucb 4.0K Feb 11 17:14 filterlogs
4.0K drwxr-xr-x 2 fran_catalan ucb 4.0K Feb 11 17:14 rmdupslogs

./logs/filterlogs:
total 8.0K
4.0K -rw-r--r-- 1 fran_catalan ucb 22 Feb 11 22:35 barcodes.1.filter.log
4.0K -rw-r--r-- 1 fran_catalan ucb 21 Feb 11 22:35 barcodes.2.filter.log

./logs/rmdupslogs:
total 8.0K
4.0K -rw-r--r-- 1 fran_catalan ucb 1.5K Feb 11 22:35 barcodes.1.rmdups.log
4.0K -rw-r--r-- 1 fran_catalan ucb 1.5K Feb 11 22:35 barcodes.2.rmdups.log

./qc:
total 8.0K
4.0K drwxr-xr-x 2 fran_catalan ucb 4.0K Feb 11 22:36 depth
4.0K drwxr-xr-x 2 fran_catalan ucb 4.0K Feb 11 17:14 quality

./qc/depth:
total 8.0K
4.0K -rw-r--r-- 1 fran_catalan ucb 50 Feb 11 22:36 barcodes.1.depth.txt
4.0K -rw-r--r-- 1 fran_catalan ucb 26 Feb 11 22:36 barcodes.2.depth.txt

./qc/quality:
total 0

Thank you in advance for your help! -Fran

caleblareau commented 3 years ago

Thanks for reporting that --skip-R didn't help-- I'll need to fix that in the next version

This Bioconductor forum looks like it should solve it if you update all of the requisite packages: https://support.bioconductor.org/p/71866/

francat commented 3 years ago

Thanks so much for your help Caleb. I ran BiocManager::valid() for the newest version of Bioconductor and that helped that issue. However, I now have a subscript out of bounds error.

Error in .subset2(x, i, exact = exact) : subscript out of bounds Calls: importMito ... importMito.explicit -> levels -> [[ -> [[.data.frame -> <Anonymous> Execution halted

Is this also an R issue?

Thanks so much for your help! We're really looking forward to using this awesome tool for our analysis. Best, Fran

francat commented 3 years ago

Hi again,

It seems running bcall works perfectly. I switched to bcall mode from tenx and it ran successfully.

Thanks again!