Error in df[, make.names(df_columns)]

[royfrancis]

I get the following error when reading in MIXCR output that was given to me.

Full output

> mr <- repLoad("data/raw/bulk-gex/GEX_mixcr")

== Step 1/3: loading repertoire files... ==

Processing "data/raw/bulk-gex/GEX_mixcr" ...
  -- [1/11] Parsing "data/raw/bulk-gex/GEX_mixcr/mixcr.sh" -- unsupported format, skipping
  -- [2/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clns" -- unsupported format, skipping
  -- [3/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.ALL.txt" -- mixcr
  -- [4/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.IGH.txt" -- mixcr
  -- [5/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.IGK.txt" -- mixcr
  -- [6/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.IGL.txt" -- mixcr
  -- [7/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.TRA.txt" -- mixcr
  -- [8/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.TRB.txt" -- mixcr
  -- [9/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.TRD.txt" -- mixcr
  -- [10/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.clonotypes.TRG.txt" -- mixcr
  -- [11/11] Parsing "data/raw/bulk-gex/GEX_mixcr/MS_GEX.matrix.tsv" -- mixcr
                                                                                                                                                                                                                      [!] Warning: can't find a column with clonal counts. Setting all clonal counts to 1.
      Did you apply repLoad to MiXCR file *_alignments.txt? If so please consider moving all *.clonotypes.*.txt MiXCR files to a separate folder and apply repLoad to the folder.
      Note: The *_alignments.txt file IS NOT a repertoire file suitable for any analysis.
Error in `df[, make.names(df_columns)]`:
! Can't subset columns that don't exist.
✖ Columns `NA.` and `NA.` don't exist.
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
In readLines(f, 1) : line 1 appears to contain an embedded nul

I have the following files as MIXCR output:

├── MS_GEX.clns
├── MS_GEX.clonotypes.ALL.txt
├── MS_GEX.clonotypes.IGH.txt
├── MS_GEX.clonotypes.IGK.txt
├── MS_GEX.clonotypes.IGL.txt
├── MS_GEX.clonotypes.TRA.txt
├── MS_GEX.clonotypes.TRB.txt
├── MS_GEX.clonotypes.TRD.txt
├── MS_GEX.clonotypes.TRG.txt
├── MS_GEX.matrix.tsv
├── MS_GEX.report
├── MS_GEX.vdjca
└── mixcr.sh

The input to MIXCR was zUMIs output from SS3 data.

> packageVersion("immunarch")
[1] ‘0.9.0’

[royfrancis]

It worked when I tried loading individual file:

mr <- repLoad("data/raw/bulk-vdj/mixcr/MS_lesion_merged.clonotypes.ALL.txt")