segfault in combineTCR

[wrb2012]

combined.TCR <- scRepertoire::combineTCR(contig.list, 
                           samples =c('pbmc_7'))


 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: rcppConstructConDfAndParseTCR(data2 %>% arrange(., chain, cdr3_nt),     unique(data2[[1]]))
 2: .constructConDfAndParseTCR(data2)
 3: scRepertoire::combineTCR(contig.list, samples = c("pbmc_7"),     removeNA = TRUE)

head(contig.list[[1]])

     barcode chain reads      v_gene      d_gene   j_gene c_gene
263  1203669   IGH     3 IGHV4-39*01 IGHD3-10*01 IGHJ3*02       
578  2718588   IGH     3 IGHV3-23*01 IGHD6-13*01 IGHJ4*02  IGHG2
780  3977376   IGH     3 IGHV3-33*01 IGHD6-19*01 IGHJ4*02  IGHA2
1249 6201652   IGH     3 IGHV3-23*01 IGHD6-19*01 IGHJ4*02       
1752 8684780   IGH     3 IGHV3-23*01 IGHD3-16*02 IGHJ4*02       
2031 9989088   IGH     3 IGHV3-30*07  IGHD3-3*01 IGHJ4*02       
                                                       cdr3_nt
263  TGTGCGAGACGTTTCACCGTATTATTCGGGGAGCTATCTGATGGTTTTGATATCTGG
578        TGCGCGAAAAATGGTCAATGGGGCAGCAGCCTAGGGGACTTAGACTACTGG
780              TGTGTGACAGACCCACCTAACAGTGGCTTCAAATTTGACTCCTGG
1249             TGTGTGACAGACCCACCTAACAGTGGCTTCAAATTTGACTCCTGG
1752                TGTGCGAAAGATTCCTGGAGCACTTCGTTAGGGGACTACTGG
2031             TGTGCGAGTGATCCCCCTGGGAGTGGTTTTTCGTTTGCCTACTGG
                    cdr3
263  CARRFTVLFGELSDGFDIW
578    CAKNGQWGSSLGDLDYW
780      CVTDPPNSGFKFDSW
1249     CVTDPPNSGFKFDSW
1752      CAKDSWSTSLGDYW
2031      CE*SPWEWFFVCLL

[ncborcherding]

Hey wrb2012,

thanks for reaching out - could you provide more information on the type of data and version of scRepertoire you are using?

Also it looks like you might be trying to use combineTCR() for BCR data?

Nick

[ncborcherding]

I am closing this issue due to lack of response - please feel free to re-open if new information is provided. Also if anyone is having the same issue, please include a reproducible example.

Thanks,
Nick