zhongll19
commented
2 years ago To all, I had the same problem, after using immdata1 <- repLoad('/data/path') immdata <- repLoad('/data/Analysis/VDJ_tcr/Diversity/data',.coding = TRUE)
== Step 1/3: loading repertoire files... ==
Processing "/data/Analysis/zhongll/VDJ_tcr/Diversity/data" ... -- [1/4] Parsing "/data/Analysis/VDJ_tcr/Diversity/data/HGSOC_1.csv" -- 10x (filt.contigs) -- [2/4] Parsing "/data/Analysis/VDJ_tcr/Diversity/data/HGSOC_2.csv" -- 10x (filt.contigs) -- [3/4] Parsing "/data/Analysis/VDJ_tcr/Diversity/data/HGSOC_3.csv" -- 10x (filt.contigs) -- [4/4] Parsing "/data/Analysis/VDJ_tcr/Diversity/data/metadata.txt" -- metadata
== Step 2/3: checking metadata files and merging files... ==
Processing "/data/Analysis/VDJ_tcr/Diversity/data" ... -- Everything is OK!
== Step 3/3: processing paired chain data... ==
Done!
Warning messages: 1: The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,fwr1,fwr1_nt,cdr1,cdr1_nt,fwr2,fwr2_nt,cdr2,cdr2_nt,fwr3,fwr3_nt,cdr3,cdr3_nt,fwr4,fwr4_nt,reads,umis,raw_clonotype_id,raw_consensus_id,exact_subclonotype_id 2: The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,fwr1,fwr1_nt,cdr1,cdr1_nt,fwr2,fwr2_nt,cdr2,cdr2_nt,fwr3,fwr3_nt,cdr3,cdr3_nt,fwr4,fwr4_nt,reads,umis,raw_clonotype_id,raw_consensus_id,exact_subclonotype_id 3: The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,fwr1,fwr1_nt,cdr1,cdr1_nt,fwr2,fwr2_nt,cdr2,cdr2_nt,fwr3,fwr3_nt,cdr3,cdr3_nt,fwr4,fwr4_nt,reads,umis,raw_clonotype_id,raw_consensus_id,exact_subclonotype_id
Import data also changed, V.name and J.name appear as semicolon-separated names，like this： Clones Proportion 1 45 0.011703511 2 27 0.007022107 CDR3.nt 1 TGTGCTCTGAGGTCCCTTAGGGAAACCAGTGGCTCTAGGTTGACCTTT;TGTGCCAGCAGTGACCGGGACCCTAGGGATACGCAGTATTTT 2 TGTGCTGTGGGAGGGAACTTCAACAAATTTTACTTT CDR3.aa V.name D.name J.name V.end 1 CALRSLRETSGSRLTF;CASSDRDPRDTQYF TRAV19;TRBV6-5 None;None TRAJ58;TRBJ2-3 NA 2 CAVGGNFNKFYF TRAV2 None TRAJ21 NA D.start D.end J.start VJ.ins VD.ins DJ.ins 1 NA NA NA NA NA NA 2 NA NA NA NA NA NA Sequence 1 TGTGCTCTGAGGTCCCTTAGGGAAACCAGTGGCTCTAGGTTGACCTTT;TGTGCCAGCAGTGACCGGGACCCTAGGGATACGCAGTATTTT 2 TGTGCTGTGGGAGGGAACTTCAACAAATTTTACTTT chain 1 TRA;TRB 2 TRA
packageVersion('immunarch') [1] ‘0.6.8’
But，When the Version=0.3.3 , there is no problem .
To all,
I just load the TCR data from 10X using repLoad, but the warning massage returns;
Warning message: The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id
This is my code to load data; immdata_10x <- repLoad("/home/users/TCR/filtered_contig_annotations.csv")
what can be the problem?