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VanLoo-lab / CAMDAC

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Error in write_fst(df_merged, f_nm) : There was an error creating the file, please check path #6

Closed MoniDR closed 1 year ago

MoniDR commented 1 year ago

Hi there,

I've come across CAMDAC and I was really excited as I think it would be a great resource to analyze our DNA methylation data - I'm particularly interested in using it to call CNVs on the data (thank you and congrats on this really nice work!).

In the first instance I've been trying to run it using the test bam files provided by you on github, to familiarize myself with the tool and its outputs, but it seems like the write_fst() keeps throwing the same error (see issue header). Below, the code I'm running (taken from the available CAMDAC user manual):

CAMDAC::pipeline_tumor_normal(
  patient_id="P1",
  tumor_id="T",
  normal_id="N",
  tumor_bam=tumor_bam,
  normal_bam=normal_bam,
  sex="XY",
  path="results/",
  pipeline_files="/path/to/pipeline_files_directory",
  build="hg38",
  min_tumor = 1, # Minimum coverage
  min_normal = 10, # Minimum coverage
  mq = 0 # Minimum mapping quality
)

I've then tried to modify the get_allele_count() function and replaced write_fst() -> writeRDS() and, despite some warnings, I was able to generate the final output CHR chrom start end width POS ref alt alt_counts ref_counts total_counts BAF total_depth M UM total_counts_m m CCGG 1 chr1 1 10496 10499 4 NA NA NA NA NA 6 5 1 6 0.8333333 6 2 chr1 1 10505 10505 1 10505 A T 0 6 6 0 6 NA NA NA NA 0 3 chr1 1 10511 10511 1 10511 G A 0 6 6 0 6 NA NA NA NA 0 4 chr1 1 10525 10526 2 NA NA NA NA NA 6 6 0 6 1.0000000 0 5 chr1 1 10539 10539 1 10539 C A 0 6 6 0 6 NA NA NA NA 0 6 chr1 1 10563 10564 2 NA NA NA NA NA 6 6 0 6 1.0000000 0

I've tried several things, but I can't really work out why the write_fst() function wouldn't work - is there anything that I'm missing? I was hoping you might be able to help and advise on this issue?

Thanks so much for your help! Monica

p.s. below session info

Session info ─────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.2 (2022-10-31)
 os       macOS Ventura 13.3.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/London
 date     2023-05-12
 rstudio  2023.03.0+386 Cherry Blossom (desktop)
 pandoc   NA

Packages
─────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 ASCAT                * 2.5.3     2023-05-12 [1] Github (VanLoo-Lab/ascat@418e1f5)
 Biobase              * 2.58.0    2022-11-07 [1] Bioconductor
 BiocGenerics         * 0.44.0    2022-11-07 [1] Bioconductor
 BiocParallel           1.32.5    2022-12-25 [1] Bioconductor
 Biostrings           * 2.66.0    2022-11-07 [1] Bioconductor
 bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.2.0)
 cachem                 1.0.6     2021-08-19 [1] CRAN (R 4.2.0)
 callr                  3.7.3     2022-11-02 [1] CRAN (R 4.2.0)
 CAMDAC               * 0.1.0     2023-05-12 [1] Github (VanLoo-lab/CAMDAC@287cfd0)
 cli                    3.6.0     2023-01-09 [1] CRAN (R 4.2.2)
 codetools              0.2-19    2023-02-01 [1] CRAN (R 4.2.0)
 colorspace             2.1-0     2023-01-23 [1] CRAN (R 4.2.0)
 crayon                 1.5.2     2022-09-29 [1] CRAN (R 4.2.0)
 curl                   5.0.0     2023-01-12 [1] CRAN (R 4.2.0)
 data.table           * 1.14.6    2022-11-16 [1] CRAN (R 4.2.0)
 DelayedArray           0.24.0    2022-11-07 [1] Bioconductor
 devtools             * 2.4.5     2022-10-11 [1] CRAN (R 4.2.0)
 digest                 0.6.31    2022-12-11 [1] CRAN (R 4.2.0)
 doParallel           * 1.0.17    2022-02-07 [1] CRAN (R 4.2.0)
 dplyr                * 1.1.0     2023-01-29 [1] CRAN (R 4.2.0)
 ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.2.0)
 fansi                  1.0.4     2023-01-22 [1] CRAN (R 4.2.0)
 fastmap                1.1.0     2021-01-25 [1] CRAN (R 4.2.0)
 foreach              * 1.5.2     2022-02-02 [1] CRAN (R 4.2.0)
 fs                   * 1.6.1     2023-02-06 [1] CRAN (R 4.2.0)
 fst                  * 0.9.8     2022-02-08 [1] CRAN (R 4.2.0)
 fstcore              * 0.9.14    2023-01-12 [1] CRAN (R 4.2.0)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.9    2023-02-05 [1] Bioconductor
 GenomeInfoDbData       1.2.9     2023-01-16 [1] Bioconductor
 GenomicAlignments    * 1.34.0    2022-11-07 [1] Bioconductor
 GenomicRanges        * 1.50.2    2022-12-18 [1] Bioconductor
 ggplot2              * 3.4.0     2022-11-04 [1] CRAN (R 4.2.0)
 glue                   1.6.2     2022-02-24 [1] CRAN (R 4.2.0)
 gridExtra            * 2.3       2017-09-09 [1] CRAN (R 4.2.0)
 gtable               * 0.3.1     2022-09-01 [1] CRAN (R 4.2.0)
 hms                    1.1.2     2022-08-19 [1] CRAN (R 4.2.0)
 htmltools              0.5.4     2022-12-07 [1] CRAN (R 4.2.0)
 htmlwidgets            1.6.1     2023-01-07 [1] CRAN (R 4.2.0)
 httpuv                 1.6.8     2023-01-12 [1] CRAN (R 4.2.0)
 IRanges              * 2.32.0    2022-11-07 [1] Bioconductor
 iterators            * 1.0.14    2022-02-05 [1] CRAN (R 4.2.0)
 later                  1.3.0     2021-08-18 [1] CRAN (R 4.2.0)
 lattice                0.20-45   2021-09-22 [1] CRAN (R 4.2.2)
 lifecycle              1.0.3     2022-10-07 [1] CRAN (R 4.2.0)
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.2.0)
 Matrix                 1.5-3     2022-11-11 [1] CRAN (R 4.2.0)
 MatrixGenerics       * 1.10.0    2022-11-07 [1] Bioconductor
 matrixStats          * 0.63.0    2022-11-18 [1] CRAN (R 4.2.0)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.2.0)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                 0.1.1.1   2018-05-18 [1] CRAN (R 4.2.0)
 munsell                0.5.0     2018-06-12 [1] CRAN (R 4.2.0)
 pillar                 1.8.1     2022-08-19 [1] CRAN (R 4.2.0)
 pkgbuild               1.4.0     2022-11-27 [1] CRAN (R 4.2.0)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.2.0)
 pkgload                1.3.2     2022-11-16 [1] CRAN (R 4.2.0)
 png                  * 0.1-8     2022-11-29 [1] CRAN (R 4.2.0)
 prettyunits            1.1.1     2020-01-24 [1] CRAN (R 4.2.0)
 processx               3.8.0     2022-10-26 [1] CRAN (R 4.2.0)
 profvis                0.3.7     2020-11-02 [1] CRAN (R 4.2.0)
 promises               1.2.0.1   2021-02-11 [1] CRAN (R 4.2.0)
 ps                     1.7.2     2022-10-26 [1] CRAN (R 4.2.0)
 purrr                  1.0.1     2023-01-10 [1] CRAN (R 4.2.0)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.2.0)
 RColorBrewer         * 1.1-3     2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp                   1.0.10    2023-01-22 [1] CRAN (R 4.2.0)
 RCurl                  1.98-1.10 2023-01-27 [1] CRAN (R 4.2.0)
 readr                * 2.1.3     2022-10-01 [1] CRAN (R 4.2.0)
 remotes                2.4.2     2021-11-30 [1] CRAN (R 4.2.0)
 rlang                  1.1.0     2023-03-14 [1] CRAN (R 4.2.0)
 Rsamtools            * 2.14.0    2022-11-07 [1] Bioconductor
 rstudioapi             0.14      2022-08-22 [1] CRAN (R 4.2.0)
 S4Vectors            * 0.36.1    2022-12-07 [1] Bioconductor
 scales               * 1.2.1     2022-08-20 [1] CRAN (R 4.2.0)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.2.0)
 shiny                  1.7.4     2022-12-15 [1] CRAN (R 4.2.0)
 stringi                1.7.12    2023-01-11 [1] CRAN (R 4.2.0)
 stringr              * 1.5.0     2022-12-02 [1] CRAN (R 4.2.0)
 SummarizedExperiment * 1.28.0    2022-11-07 [1] Bioconductor
 tibble                 3.2.1     2023-03-20 [1] CRAN (R 4.2.0)
 tidyselect             1.2.0     2022-10-10 [1] CRAN (R 4.2.0)
 tzdb                   0.3.0     2022-03-28 [1] CRAN (R 4.2.0)
 urlchecker             1.0.1     2021-11-30 [1] CRAN (R 4.2.0)
 usethis              * 2.1.6     2022-05-25 [1] CRAN (R 4.2.0)
 utf8                   1.2.3     2023-01-31 [1] CRAN (R 4.2.0)
 vctrs                  0.6.2     2023-04-19 [1] CRAN (R 4.2.0)
 withr                  2.5.0     2022-03-03 [1] CRAN (R 4.2.0)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.2.0)
 XVector              * 0.38.0    2022-11-07 [1] Bioconductor
 zlibbioc               1.44.0    2022-11-07 [1] Bioconductor
NMNS93 commented 1 year ago

Hi Monica,

Thanks for raising this issue! It should now be resolved. Please also note that the test arguments have changed slightly. Let us know if you run into any trouble, and any general feedback on the tool is also welcome.

Best,

Nana