`load10x` can't find `clusters.csv` in CellRanger 7.1.0 output
Closed this issue · 1 comments
aseyedia commented
I'm trying to load in some output from CR count
7.1.0 and it can't automatically load the cluster information even though it's exactly where it's supposed to be in v7 CellRanger outputs. I'm definitely using SoupX 1.6.1.
Line 64 in 8d89492
> file.exists("code/03-count/HTS-SO21-07-NLP1-5p-GEX_count/outs/analysis/clustering/gene_expression_graphclust/clusters.csv")
[1] TRUE
> for (i in 1:length(sc)) {
+ sc[[i]] <- autoEstCont(sc[[i]], soupQuantile = 0.5)
+ sc[[i]] <- adjustCounts(sc[[i]])
+ }
Error in autoEstCont(sc[[i]], soupQuantile = 0.5) :
Clustering information must be supplied, run setClusters first.
I am, however, able to get the cluster info using setClusters
:
clusters <- lapply(Sys.glob(paste0("code/03-count/*/outs/analysis/clustering/gene_expression_graphclust/clusters.csv")), read.csv)
for (i in 1:length(sc)) {
sc[[i]] <- setClusters(sc[[i]], clusters[[i]]$Cluster)
}
I'm using R 4.1.2. Here's my session_info
in case you need it:
> sessioninfo::session_info()
System has not been booted with systemd as init system (PID 1). Can't operate.
Failed to create bus connection: Host is down
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.1.2 (2021-11-01)
os Red Hat Enterprise Linux 8.2 (Ootpa)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-02-07
rstudio 99.9.9 Juliet Rose (server)
pandoc NA
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
! package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.2)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.2)
R cli 3.2.0 <NA> [2] <NA>
cluster 2.1.2 2021-04-17 [2] CRAN (R 4.1.2)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.2)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.1.2)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.2)
data.table 1.14.6 2022-11-16 [1] CRAN (R 4.1.2)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.2)
deldir 1.0-6 2021-10-23 [1] CRAN (R 4.1.2)
digest 0.6.30 2022-10-18 [1] CRAN (R 4.1.2)
dplyr 1.0.8 2022-02-08 [1] CRAN (R 4.1.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.2)
fitdistrplus 1.1-8 2022-03-10 [1] CRAN (R 4.1.2)
future 1.29.0 2022-11-06 [1] CRAN (R 4.1.2)
future.apply 1.10.0 2022-11-05 [1] CRAN (R 4.1.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.2)
ggplot2 3.3.6 2022-05-03 [1] CRAN (R 4.1.2)
ggrepel 0.9.2 2022-11-06 [1] CRAN (R 4.1.2)
ggridges 0.5.4 2022-09-26 [1] CRAN (R 4.1.2)
globals 0.16.2 2022-11-21 [1] CRAN (R 4.1.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2)
goftest 1.2-3 2021-10-07 [1] CRAN (R 4.1.2)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2)
gtable 0.3.1 2022-09-01 [1] CRAN (R 4.1.2)
here * 1.0.1 2020-12-13 [1] CRAN (R 4.1.2)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.1.2)
htmlwidgets 1.6.0 2022-12-15 [1] CRAN (R 4.1.2)
httpuv 1.6.7 2022-12-14 [1] CRAN (R 4.1.2)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.1.2)
ica 1.0-3 2022-07-08 [1] CRAN (R 4.1.2)
igraph 1.3.2 2022-06-13 [1] CRAN (R 4.1.2)
irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.1.2)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.1.2)
KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.1.2)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.2)
lattice 0.20-45 2021-09-22 [2] CRAN (R 4.1.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.2)
leiden 0.4.3 2022-09-10 [1] CRAN (R 4.1.2)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
listenv 0.9.0 2022-12-16 [1] CRAN (R 4.1.2)
lmtest 0.9-40 2022-03-21 [1] CRAN (R 4.1.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.2)
MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.2)
Matrix * 1.5-3 2022-11-11 [1] CRAN (R 4.1.2)
matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.1.2)
mgcv 1.8-38 2021-10-06 [2] CRAN (R 4.1.2)
mime 0.12 2021-09-28 [1] CRAN (R 4.1.2)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.1.2)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.2)
nlme 3.1-153 2021-09-07 [2] CRAN (R 4.1.2)
parallelly 1.33.0 2022-12-14 [1] CRAN (R 4.1.2)
patchwork 1.1.2 2022-08-19 [1] CRAN (R 4.1.2)
pbapply 1.6-0 2022-11-16 [1] CRAN (R 4.1.2)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.2)
R plotly 4.10.0 <NA> [2] <NA>
plyr 1.8.7 2022-03-24 [1] CRAN (R 4.1.2)
png 0.1-8 2022-11-29 [1] CRAN (R 4.1.2)
polyclip 1.10-4 2022-10-20 [1] CRAN (R 4.1.2)
progressr 0.12.0 2022-12-13 [1] CRAN (R 4.1.2)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.2)
purrr 0.3.5 2022-10-06 [1] CRAN (R 4.1.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2)
RANN 2.6.1 2019-01-08 [1] CRAN (R 4.1.2)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.2)
Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.1.2)
RcppAnnoy 0.0.20 2022-10-27 [1] CRAN (R 4.1.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2)
reticulate 1.25 2022-05-11 [1] CRAN (R 4.1.2)
rgeos 0.6-1 2022-12-14 [1] CRAN (R 4.1.2)
R rlang 1.0.2 <NA> [2] <NA>
ROCR 1.0-11 2020-05-02 [1] CRAN (R 4.1.2)
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.2)
rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.1.2)
Rtsne 0.16 2022-04-17 [1] CRAN (R 4.1.2)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.1.2)
scattermore 0.8 2022-02-14 [1] CRAN (R 4.1.2)
sctransform 0.3.5 2022-09-21 [1] CRAN (R 4.1.2)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
Seurat * 4.1.1 2022-05-02 [1] CRAN (R 4.1.2)
SeuratObject * 4.1.0 2022-05-01 [1] CRAN (R 4.1.2)
shiny 1.7.4 2022-12-15 [1] CRAN (R 4.1.2)
SoupX * 1.6.1 2022-05-26 [1] CRAN (R 4.1.2)
sp * 1.5-1 2022-11-07 [1] CRAN (R 4.1.2)
spatstat.core 2.4-0 2022-02-15 [1] CRAN (R 4.1.2)
spatstat.data 2.2-0 2022-04-18 [1] CRAN (R 4.1.2)
spatstat.geom 2.3-2 2022-02-12 [1] CRAN (R 4.1.2)
spatstat.random 2.1-0 2022-02-12 [1] CRAN (R 4.1.2)
spatstat.sparse 2.1-1 2022-04-18 [1] CRAN (R 4.1.2)
spatstat.utils 2.3-1 2022-05-06 [1] CRAN (R 4.1.2)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2)
stringr 1.4.1 2022-08-20 [1] CRAN (R 4.1.2)
survival 3.2-13 2021-08-24 [2] CRAN (R 4.1.2)
tensor 1.5 2012-05-05 [1] CRAN (R 4.1.2)
tibble 3.1.7 2022-05-03 [1] CRAN (R 4.1.2)
tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.2)
uwot 0.1.14 2022-08-22 [1] CRAN (R 4.1.2)
vctrs 0.4.0 2022-03-30 [1] CRAN (R 4.1.2)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.1.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.2)
zoo 1.8-10 2022-04-15 [1] CRAN (R 4.1.2)
[1] /home/seyediana/R/x86_64-pc-linux-gnu-library/4.1
[2] /cm/shared/apps_chop/R/4.1.2/lib64/R/library
R ── Package was removed from disk.
EDePasquale commented
I have the same issue with Cell Ranger 7, and the work around provided by aseyedia works just fine (thank you!), but I would like to see this get fixed too. Thanks!