souporcell: clusters_tmp.tsv is empty which caused subprocess.CalledProcessError

Hello, When I was running souporcell_pipeline.py by setting the parameter -k 15 which could be a potential problem, I got a subporcess.CalledProcessError when it went to the function “doublets(args, ref_mtx, alt_mtx, cluster_file)”. By the information of Traceback, I found that after the function “souporcell(args, ref_mtx, alt_mtx, final_vcf)” was run, the “cluster_file” which was named “clusters_tmp.tsv” in the output directory is empty. I think this might caused the function “doublets(args, ref_mtx, alt_mtx, cluster_file)” went wrong which need the “cluster_file” as input. But now I don’t know how to deal with it.

running souporcell doublet detection Traceback (most recent call last) : File “/opt/souporcell/souporcell_pipeline.py”, line 596, in <module> doublets(args, ref_mtx, alt_mtx, cluster_file) File “/opt/souporcell/souporcell_pipeline.py”, line 541, in doublets subprocess.check_call([directory+“/troublet/target/release/troublet”, “–alts”, alt_mtx, “–refs”, ref_mtx, “–clusters”, cluster_file], stdout = dub, stderr = err) File “/usr/local/envs/py36/lib/python3.6/subprocess.py”, line 311, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command ‘[’/opt/souporcell/troublet/target/release/troublet’, ‘–alts’, ‘/home/pro5/results/alt.mtx’, ‘–refs’, ‘/home/pro5/results/ref.mtx’, ‘–clusters’, ‘/home/pro5/results/clusters_tmp.tsv’]’ returned non-zero exit status 101.

By the way, when I checked the doublets.err file, I got something that I don’t know what it means.

thread ‘main’ panicked at ‘index out of bounds: the len is 0 but the index is 111406’, src/main.rs:328:22 note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

Thanks a lot!