Issue with cellsnp-lite Running in Single-Thread Mode

[parv-sachdeva]

Hi,

I'm encountering an issue when trying to run cellsnp-lite in mode 2b on a BAM file. The application only launches a [Thread-0] and does not spawn additional threads. This problem also occurs in other modes.

Here is the command I used:

cellsnp-lite -s subset_X.bam -O subset_X_2b -p 10 --minMAF 0.1 --minCOUNT 20 --cellTAG None --UMItag UB --chrom chrX --gzip

Despite specifying -p 10 for multiple threads, it seems to be running in single-thread mode. Could you provide any guidance on why this might be happening and how to resolve it?

For reference, I installed the latest version of cellsnp-lite using CMake: cellsnp-lite 1.2.3 (htslib 1.20).

Tagging @wvictor14 for reference.

Thank you for your assistance!

Best,
Parv Sachdeva

[hxj5]

Hi Parv,

Thanks for the question and detailed information. Unfortunately, in mode 2 (whole chromosome pileup), multi-threading can only be utilized when there are multiple input chromosomes such that each chromosome would be assigned to one thread. In your case, single chromosome "chrX" can only allocate (at most) one thread. See also issue #40 and #111.

Best,
Xianjie