Open ahoffrichter opened 1 year ago
Hi, the files in the output folder should probably be the temporary files (with suffix such as .0
, .1
, ... etc). When the program finishes, the output folder should look like this example.
How many cells does the bam file contain? Sometimes it could take a long time for cellsnp-lite to genotype a big dataset, especially in mode 2a (i.e., to pileup whole chromosomes for 10x data). Could you also share your command line and the version of cellsnp-lite?
Best, Xianjie
Hi, the bam file should contain about 15,600 cells. I used mode 1a with the region vcf from here. I'm running this on a cluster with cellsnp-lite version 1.2.2. I'm not exactly sure what you mean with "share your command line".
Best, Anne
The command line contains all the parameters you used to run cellsnp-lite, e.g.,
cellsnp-lite -s $BAM -b $BARCODE -O $OUT_DIR -R $REGION_VCF -p 20 --minMAF 0.1 --minCOUNT 20 --gzip
.
The 15,600 cells indicate the bam is probably a big 10x dataset. To speedup, you may
filtered_gene_bc_matrices
instead of from raw_gene_bc_matrices
in the cellranger output folder (update -b);AF5e2
VCF file instead of AF5e4
in this folder (update -R);Ah ok, the command I used looks like this:
cellsnp-lite -s path/to/possorted_genome_bam.bam -b /path/to/raw_feature_bc_matrix/barcodes.tsv.gz -O /vireo/test -R /vireo/genome1K.phase3.SNP_AF5e2.chr1toX.hg38.vcf.gz -p 20 --minMAF 0.1 --minCOUNT 20 --gzip
Yes indeed, it is a 10x dataset and I used the raw barcodes. I will try out your suggestions, thank you very much for your help!
For 15k cells, roughly how long did this take to run?
hello, i ran cellsnp-lite, and it failed with"[E::idx_find_and_load] Could not retrieve index file for '/h/sunnan/VKHDATA/vkha/gex_possorted_bam.bam'", what should i do next? thank you very much!
Hi, I ran cellsnp-lite with one bam file. It is now already running since 3 weeks. I was wondering if this is to be expected. Is there somewhere any information on the expected output files? There are already several files in my output folder and I am not sure if the program is actually already finished and it just appears as still running. Best, Anne