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single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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installation issue #15

Closed AnjaliC4 closed 3 years ago

AnjaliC4 commented 3 years ago

Hi, I am working on a cluster environment, and activated conda and installed cellsnp-lite, which executes cellsnp-lite --help and shows me the options, so it got successfully installed, but when actually running this, it gives me a segmentation fault. Please help!

cellsnp-lite -s /scratch/graham_atac_analysis/merged_55_371_bam/merged_173_397.bam -b /scratch/graham_atac_analysis/merged_55_371_bam/barcodes_173_397.shuf -O /scratch/graham_atac_analysis/merged_55_371_bam/snp2/snp_chrx --minMAF 0.1 -p 22 --chrom chrX

[I::main] start time: 2021-04-01 18:16:34 [I::main] mode2: pileup 22 whole chromosomes in 3345 single cells. [E::csp_mplp_prepare] failed to set sample names. [E::csp_pileup_core] could not prepare csp_mplp_t structure. Segmentation fault

hxj5 commented 3 years ago

Hi, thanks for your feedback. Seems barcodes could be wrong. Could you show a few lines of your barcode file and check if there were duplicate barcodes?

Was the latest version (v1.2.0) of cellsnp-lite you were using? you could check with cellsnp-lite -V

Xianjie

AnjaliC4 commented 3 years ago

Hi, thanks for the feedback. You are correct, the barcodes were duplicates. I have appended "-1" "-2" to them to keep them separate, and now it works.