I have been trying to run cite-seq-count on my data but haven't been successful so far.
I tried initially on the cluster but then gave up and tried locally. On the cluster, the job was never finishing so had to abort. In the error file there was this message:
No local minima was accepted. Recommend checking the plot output and counts per local minima (requires `--plot-prefix` option) and then re-running with manually selected threshold (`--set-cell-number` option)
Unable to revert mtime: /Library/Fonts
Unable to revert mtime: /Library/Fonts/Microsoft
Counting number of reads
Started mapping
CITE-seq-Count is running with 4 cores.
Processed 1,000,000 reads in 23.67 seconds. Total reads: 1,000,000 in child 29798
Processed 1,000,000 reads in 39.92 seconds. Total reads: 1,000,000 in child 29799
Mapping done for process 29798. Processed 1,969,487 reads
Processed 1,000,000 reads in 1.0 minute, 2.679 seconds. Total reads: 1,000,000 in child 29801
Mapping done for process 29799. Processed 1,969,487 reads
Mapping done for process 29801. Processed 1,969,487 reads
Processed 1,000,000 reads in 1.0 minute, 30.52 seconds. Total reads: 1,000,000 in child 29800
Mapping done for process 29800. Processed 1,969,487 reads
Mapping done
Merging results
Correcting cell barcodes
ERROR:root:No local minima was accepted. Recommend checking the plot output and counts per local minima (requires `--plot-prefix` option) and then re-running with manually selected threshold (`--set-cell-number` option)
Could not find a good local minima for correction.
No cell barcode correction was done.
Correcting umis
I installed cite-seq-count version 1.4.1, with python 3.7.0.
Any help would be much appreciated.