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jon-xu / scSplit

Genotype-free demultiplexing of pooled single-cell RNA-Seq, using a hidden state model for identifying genetically distinct samples within a mixed population.
MIT License
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scSplit ends silently #16

Closed achernom closed 2 years ago

achernom commented 2 years ago

Hi, I am trying to run scSplit on snRNA seq mouse data. Unfortunately the program ends unexpectedly (no output files ) without any error nor warning messages. Here is my command-line: ~/Downloads/scSplit/scSplit counts -v DG-003-filt.vcf.gz -i DG-003_S2/filteredBAMforPileUp.bam -b 3M-february-2018.txt --tag CR -r ref_filtered.csv -a alt_filtered.csv -o results

Perhaps I should mention that I installed the required packages using pip3 (I am not a python user), but I got some weird linker messages that appeared after import vcf: >>>import vcf Error: package or namespace load failred for "methods" in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object ¨/usr/local/lib/R/library/methods/libs/methods.so": libR.so: cannot open shared object file: No such file or directory

After setting the environmental LD_LIBRARY_PATH variable the error dissapeared. Any help will be very wellcome! Ariel

jon-xu commented 2 years ago

Hi Ariel, Could you try gunzip your vcf file first before counting? Jon

achernom commented 2 years ago

Hi Jon, Thanks for your prompt response. The problem persists with the plain text vcf A

jon-xu commented 2 years ago

Hi Ariel,

Did you use the barcode whitelist downloaded from 10x website? That's the full whitelist from 10x experiments. Here you need to use the barcode list from the result of your 10x cellranger run (filtered one).

Hope it helps. Jon

achernom commented 2 years ago

Hi Jon, Just to close this issue...I found the cause of the problem ... I was invoking scSplit using scSplit counts instead of scSplit count (ay!). Anyway...thanks for your support Ariel