Enter the body of text here

Code should be placed in three backticks as shown below

se <- tximeta(coldata)
Error in parse_con(txt, bigint_as_char) : 
  lexical error: invalid char in json text.
          d": 0,     "percent_mapped": NaN,     "call": "quant",     "
                     (right here) ------^
sessionInfo( )

R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.5.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] PCAtools_2.8.0              ggrepel_0.9.1               DESeq2_1.36.0               org.Hs.eg.db_3.15.0         org.Mm.eg.db_3.15.0         AnnotationDbi_1.58.0       
 [7] forcats_0.5.2               stringr_1.4.1               dplyr_1.0.9                 purrr_0.3.4                 tidyr_1.2.0                 tibble_3.1.8               
[13] ggplot2_3.3.6               tidyverse_1.3.2             SummarizedExperiment_1.26.1 Biobase_2.56.0              GenomicRanges_1.48.0        GenomeInfoDb_1.32.3        
[19] IRanges_2.30.1              S4Vectors_0.34.0            BiocGenerics_0.42.0         MatrixGenerics_1.8.1        matrixStats_0.62.0          biomaRt_2.52.0             
[25] tximeta_1.14.1              readr_2.1.2                

loaded via a namespace (and not attached):
  [1] readxl_1.4.1                  backports_1.4.1               AnnotationHub_3.4.0           BiocFileCache_2.4.0           plyr_1.8.7                    lazyeval_0.2.2               
  [7] splines_4.2.1                 BiocParallel_1.30.3           digest_0.6.29                 ensembldb_2.20.2              htmltools_0.5.3               fansi_1.0.3                  
 [13] magrittr_2.0.3                memoise_2.0.1                 ScaledMatrix_1.4.0            googlesheets4_1.0.1           tzdb_0.3.0                    Biostrings_2.64.1            
 [19] annotate_1.74.0               modelr_0.1.9                  prettyunits_1.1.1             colorspace_2.0-3              blob_1.2.3                    rvest_1.0.3                  
 [25] rappdirs_0.3.3                haven_2.5.1                   crayon_1.5.1                  RCurl_1.98-1.8                jsonlite_1.8.0                tximport_1.24.0              
 [31] genefilter_1.78.0             survival_3.4-0                glue_1.6.2                    gtable_0.3.0                  gargle_1.2.0                  zlibbioc_1.42.0              
 [37] XVector_0.36.0                DelayedArray_0.22.0           BiocSingular_1.12.0           scales_1.2.1                  DBI_1.1.3                     Rcpp_1.0.9                   
 [43] xtable_1.8-4                  progress_1.2.2                dqrng_0.3.0                   bit_4.0.4                     rsvd_1.0.5                    httr_1.4.4                   
 [49] RColorBrewer_1.1-3            ellipsis_0.3.2                pkgconfig_2.0.3               XML_3.99-0.10                 dbplyr_2.2.1                  locfit_1.5-9.6               
 [55] utf8_1.2.2                    reshape2_1.4.4                tidyselect_1.1.2              rlang_1.0.4                   later_1.3.0                   munsell_0.5.0                
 [61] BiocVersion_3.15.2            cellranger_1.1.0              tools_4.2.1                   cachem_1.0.6                  cli_3.3.0                     generics_0.1.3               
 [67] RSQLite_2.2.16                broom_1.0.0                   fastmap_1.1.0                 yaml_2.3.5                    bit64_4.0.5                   fs_1.5.2                     
 [73] KEGGREST_1.36.3               AnnotationFilter_1.20.0       sparseMatrixStats_1.8.0       mime_0.12                     xml2_1.3.3                    compiler_4.2.1               
 [79] rstudioapi_0.13               filelock_1.0.2                curl_4.3.2                    png_0.1-7                     interactiveDisplayBase_1.34.0 reprex_2.0.2                 
 [85] geneplotter_1.74.0            stringi_1.7.8                 GenomicFeatures_1.48.3        lattice_0.20-45               ProtGenerics_1.28.0           Matrix_1.4-1                 
 [91] vctrs_0.4.1                   pillar_1.8.1                  lifecycle_1.0.1               BiocManager_1.30.18           cowplot_1.1.1                 bitops_1.0-7                 
 [97] irlba_2.3.5                   httpuv_1.6.5                  rtracklayer_1.56.1            R6_2.5.1                      BiocIO_1.6.0                  promises_1.2.0.1             
[103] codetools_0.2-18              assertthat_0.2.1              rjson_0.2.21                  withr_2.5.0                   GenomicAlignments_1.32.1      Rsamtools_2.12.0             
[109] GenomeInfoDbData_1.2.8        parallel_4.2.1                hms_1.1.2                     grid_4.2.1                    beachmat_2.12.0               DelayedMatrixStats_1.18.0    
[115] googledrive_2.0.0             shiny_1.7.2                   lubridate_1.8.0               restfulr_0.0.15

I found the problem, and it's not with tximeta. Despite the fastq files existing (but being empty), salmon produced a quant.sf file, and wrote into ../aux_info/meta_info.json ""percent_mapped": NaN,"

I didn't know there was an issue with that sample until tximeta couldn't parse meta_info.json.

It might have been helpful for tximeta to report which .json file had the unusable information.