findAlleles get empty clone data

[liu9756]

Hi ! I would like to run findAlleles to continue the analysis of SHM. However, when I run the findAlleles command with my own data which generated from analysis, no clone information is detected in by findAlleles. I am sure the data indeed contain the clone information, so please help to check if my command is correct. Thanks!

user@user-Precision-3660:/media/user/Elements/Data_Ye_Liu/scRNA/mouse/ZSG_BCR/S6_MIXC_result_kit2$ mixcr findAlleles -OfilterForDataWithUmi.useClonesWithCountGreaterThen=0 --report DCh.findAlleles.report.txt --export-alleles-mutations DCh_alleles.tsv --export-library DCh_alleles.json --output-template S6.reassigned.clns *.clns IMPORTANT: MiXCR will use at most 6373MB of RAM, use -Xmx to change automatically set heap size (i.e. -Xmx50g to set heap size to 50 Gb) WARNING: unnecessary override -OuseClonesWithCountGreaterThen=0 with the same value. Step 1 of 7: count diversity for dataset: progress unknown Step 2 of 7: grouping by the same J gene: progress unknown Step 2 of 7: Searching for J alleles: progress unknown Step 3 of 7: grouping by the same V gene: progress unknown Step 4 of 7: grouping by the same J gene: progress unknown Step 5 of 7: grouping by the same V gene: progress unknown Step 6 of 7: removing unnecessary genes: progress unknown Step 7 of 7: realigning mouse_S6.clns: progress unknown ============== FindAlleles Report ============== Analysis time: 311ms Clones score delta stats: size: 0 sum: 0.0 min: NaN max: NaN avg: NaN quadratic mean: NaN std deviation: NaN Clones count with no change of score: 0 Clones count with negative score change: 0 Found alleles on first try: 0 Zygotes: {} Not enough information for allele search: [] Found alleles: 0 De novo alleles: 0 Known variant from library: 0 Not enough info for search, but aligned on known allele: 0 Not changed genes: 0 Not changed after search: 0 No clones to search: 0 Have clones to search, but not enough info for search and can't be aligned on known variant: 0 Removed genes: 617 No top hits in result files: 0 No top hits in source files: 0 Can be aligned on other gene: 0 Not represented in source files: 617 Found alleles that don't fit well to data: {}