Error: fail to write samples to cellSNP.samples.tsv

single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

https://cellsnp-lite.readthedocs.io

Apache License 2.0

125 stars 11 forks source link

Error: fail to write samples to cellSNP.samples.tsv #136

Open Wenjun-Liu opened 2 weeks ago

Wenjun-Liu commented 2 weeks ago

Hi team, thank you for developing this great tool. I tried running it but ran into a weird error where it says: fail to write samples to '/hpcfs/groups/phoenix-hpc-pololab/Mike_prostate_SNP_trail/output/cellsnp/cellSNP.samples.tsv'. But the cellSNP.samples.tsv file was generated and cell barcodes have been written into it. Any idea what I have done wrong? Thank you! Screenshot 2024-08-26 at 11 14 38 am

hxj5 commented 2 weeks ago

Hi, it seems something is wrong when loading the barcodes (more than 100M barcodes loaded) and SNPs (0 SNPs loaded). You may double check the command line, the barcode file (-b option) and the SNP file (-R option).

Alternatively, you may share more details here for debugging, including

the command line you used;
the stdout (.out logging file) and stderr (.err logging file);
a few lines of the barcode file;
a few lines of the SNP file.