Found dataframe without required column Cluster

[liu9756]

My code: #load the package into the R environment: library(immunarch) library(dplyr) file_path = "yard/run_cellranger_vdj/run_vdj_S5/outs/aim" immdata_10x <- repLoad(file_path) bcr_data <- immdata_10x$data%>% top(500) bcr_data

bcr_data %>% seqCluster(seqDist(bcr_data), .fixed_threshold = 3) bcr_data %>% repGermline(.threads = 1) bcr_data %>% repAlignLineage(.min_lineage_sequences = 2)

And I have some errors and warning:

For bcr_data %>% repGermline(.threads = 1) Warning message: In merge_reference_sequences(., reference, "V", species, sample_name) : Genes or alleles IGHV1-20;IGKV10-94, IGKV3-4, IGHV2-3;IGKV6-23;IGKV2-137, IGHV1-66;IGKV4-80, IGHV1-18;IGKV1-110, IGHV9-4;IGKV6-15, IGHV1-54;IGLV1, IGHV8-12;IGKV4-91, IGHV1-18;IGKV4-74, IGHV2-9-1;IGKV1-117, IGHV14-4;IGLV1, IGHV5-6;IGKV12-41, IGHV1-85, IGHV6-3;IGKV8-24, IGHV6-3;IGKV1-117, IGHV6-3;IGKV6-15, IGHV1-52;IGKV10-95;IGKV10-96, IGHV10-1;IGKV10-96, IGHV1-26;IGKV10-96, IGHV1-9;IGKV10-96, IGHV1-19;IGKV10-96, IGHV1-18;IGKV10-96, IGHV2-5;IGKV10-96, IGHV1-69;IGKV4-57, IGHV1-64;IGKV4-57, IGHV5-17;IGKV4-78, IGHV1-69;IGKV4-74, IGKV4-74, IGHV1-81;IGKV4-59, IGHV1-55;IGKV4-72, IGHV1-26;IGKV4-55, IGHV5-16;IGKV4-55, IGHV1-64;IGKV4-55, IGHV13-2;IGKV10-94;IGKV4-59, IGKV4-81, IGHV1-26;IGKV4-58, IGKV4-50, IGHV9-3;IGKV4-50, IGHV1-66;IGKV4-50, IGHV1-55;IGKV4-50, IGKV4-70, IGHV2-2;IGKV1-122, IGHV1-81;IGKV1-133, IGHV1-19;IGKV1-133, IGHV1-55;IGKV1-133, IGHV1-53;IGKV1-133, IGHV1-75;IGKV17-127;IGKV1-133, IGHV1-15;IGKV1-110, IGHV5-17;IGKV1-110;IGKV19-93, IGHV1-85;IGKV1-110, IGHV14-1;IGKV1-110, IGHV1-55;IGKV1-110, IGHV13-2;IGKV1-110, IGHV8-8;IGKV1-110, IGHV6-6;IGKV1-110, IGKV1-135, IGHV6-6;IGKV1-135, IGHV2-3;IGKV1-135, IGHV1-26;IGKV1-135, IGHV1-50;IGKV1-99, IGHV1-82;IGKV1-135, IGHV1-55;IGKV1-135, IGHV1-64;IGKV1-135, IGHV2-2;IGKV1-135, IGHV5-9-1;IGKV1-117, IGHV1-12;IGKV1-117, IGHV1-15;IGKV1-117, IGHV5-6;IGKV1-117, IGKV1-110, IGHV8-12;IGHV1-18;IGKV1-110, IGHV1-22;IGKV1-117, IGHV1-81;IGKV1-117;IGKV11-125, IGHV1-72;IGKV1-117, IGHV1-85;IGKV1-117, IGHV9-3;IGKV1-117, IGHV1-76;IGKV12-38, IGKV12-38, IGHV1-55;IGKV12-38, IGHV5-9-1;IGKV6-20, IGHV5-9-1;IGKV6-17, IGHV5-9-1;IGKV17-121, IGHV5-9-1;IGKV8-28, IGHV1-15;IGKV12-46, IGHV1-15;IGKV6-17, IGHV1-15;IGKV3-4, IGHV1-80;IGKV6-20, IGHV6-6;IGKV17-121, IGHV13-2, IGHV7-3;IGKV2-137, IGHV2-2;IGKV2-137, IGHV1-26;IGKV2-137, IGKV2-137, IGHV1-18;IGKV5-39, IGHV5-17;IGKV5-39, IGKV5-48, IGKV12-98, IGHV1-59;IGKV5-43, IGKV5-43, IGHV1-31;IGKV11-125;IGKV5-43, IGHV1-72;IGKV5-45, IGHV9-3;IGKV5-43, IGHV1-19;IGKV16-104, IGHV1-72;IGKV15-103, IGHV2-2;IGKV13-84, IGHV8-12;IGKV8-16;IGKV13-85, IGHV1-54;IGKV13-84, IGHV1-26;IGKV12-44, IGHV1-18;IGKV12-46, IGHV2-9;IGKV12-46, IGKV12-46, IGHV1-82;IGKV12-46, IGHV1-39;IGKV12-46, IGHV8-8;IGKV12-46, IGHV9-3;IGKV12-46, IGHV1-22;IGKV12-44, IGHV7-3;IGKV12-44, IGHV8-8;IGKV12-44, IGHV5-15;IGKV12-44, IGHV1-52;IGKV12-44, IGKV12-41, IGHV5-16;IGKV12-46, IGHV5-17;IGKV12-46, IGHV1-63;IGKV12-46, IGHV1-80;IGKV12-46, IGKV8-19, IGHV1-82;IGKV3-10, IGKV3-10, IGHV5-12;IGKV3-2, IGHV1-72;IGKV3-2, IGHV2-6;IGKV3-4, IGHV5-16;IGKV3-1, IGHV9-3;IGKV3-1, IGHV1-64;IGKV3-1, IGHV1-58;IGKV3-9, IGKV8-24, IGHV5-12;IGKV8-24, IGHV9-3;IGKV8-24, IGHV1-39;IGKV6-25, IGHV1-9;IGKV8-24, IGHV1-26;IGKV6-17, IGHV5-4;IGKV6-17, IGHV1-52;IGKV6-17, IGHV1-80;IGKV3-5, IGHV1-26;IGKV6-23, IGHV1-26;IGKV6-15, IGHV2-9-1;IGKV8-30, IGHV1-52;IGKV8-30, IGHV8-8;IGKV8-30, IGHV1-72;IGKV8-30, IGKV3-7, IGHV1-52;IGKV6-32, IGHV5-12;IGKV6-32, IGHV5-17;IGKV6-32, IGKV10-94, IGHV1-12;IGKV10-94, IGHV1-82;IGKV10-94, IGHV1-52;IGKV8-34, IGHV8-8;IGKV8-27, IGHV1-59;IGKV8-27, IGHV1-62-2;IGKV8-27, IGHV5-16;IGKV12-41, IGHV9-3;IGKV9-124, IGKV9-120, IGHV1-80;IGKV9-120, IGHV1-81;IGKV9-124, IGHV1-9;IGKV9-120, IGHV1-69;IGKV9-120, IGHV1-75;IGKV14-126, IGHV1-80;IGKV14-126, IGKV14-126, IGHV1-64;IGKV15-103, IGHV5-16;IGKV19-93, IGKV14-111, IGHV1-19;IGKV3-4, IGHV5-9, IGHV1-49;IGKV17-127, IGHV1-77;IGKV17-121, IGHV7-3, IGHV1-26, IGHV1-19;IGKV2-109, IGHV5-6, IGHV4-1, IGHV1-72, IGHV5-4, IGHV1-9;IGKV2-109, IGHV1-53, IGHV1-26;IGKV17-127, IGHV1-18;IGLV1, IGHV1-82, IGHV1-34;IGKV4-63, IGHV9-3, IGHV1-53;IGKV2-109, IGHV5-17, IGHV1-74, IGHV1-75, IGHV2-3, IGHV2-9-1, IGHV2-3;IGKV6-20, IGHV14-2;IGLV1, IGHV8-8, IGHV1-22;IGLV1, IGHV10-3;IGLV1, IGHV10-1;IGLV2, IGKV6-20, IGKV17-127 from sample filtered_contig_annotations not found in the reference and will be dropped! Probably, species argument is wrong (current value: HomoSapiens) or the data contains non-BCR genes.

For repAlignLineage: > bcr_data %>% repAlignLineage(.min_lineage_sequences = 2) Error in .function(., ...) : Found dataframe without required column Cluster; existing columns: Clones, Proportion, CDR3.nt, CDR3.aa, V.name, D.name, J.name, V.end, D.start, D.end, J.start, VJ.ins, VD.ins, DJ.ins, Sequence, chain, Barcode, raw_clonotype_id, ContigID, C.name, CDR1.nt, CDR2.nt, CDR1.aa, CDR2.aa, FR1.nt, FR2.nt, FR3.nt, FR4.nt, FR1.aa, FR2.aa, FR3.aa, FR4.aa

Another question is that I use 10x data and can only input filtered_contig_annotations