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make_bamtofastq.R
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make_bamtofastq.R
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library('sgejobs')
library('sessioninfo')
dirs <- dir(pattern = '^1')
stopifnot(length(dirs) == 12)
job_loop(
loops = list(sample = dirs),
name = 'bamtofastq',
cores = 4,
queue = 'bluejay',
memory = '20G',
create_shell = TRUE,
logdir = 'logs_bamtofastq'
)
dir.create('logs_bamtofastq', showWarnings = FALSE)
# /dcl02/lieber/ajaffe/SpatialTranscriptomics/bamtofastq-1.2.0 --nthreads=4 /dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/10X/${sample}/${sample}_mRNA.bam /dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/10X/${sample}/fastq
## Reproducibility information
print('Reproducibility information:')
Sys.time()
proc.time()
options(width = 120)
session_info()
# ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
# setting value
# version R version 3.6.1 Patched (2019-09-06 r77160)
# os CentOS Linux 7 (Core)
# system x86_64, linux-gnu
# ui X11
# language (EN)
# collate en_US.UTF-8
# ctype en_US.UTF-8
# tz US/Eastern
# date 2019-12-03
#
# ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
# package * version date lib source
# assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1)
# backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
# cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
# codetools 0.2-16 2018-12-24 [3] CRAN (R 3.6.1)
# colorout * 1.2-2 2019-09-26 [1] Github (jalvesaq/colorout@641ed38)
# colorspace 1.4-1 2019-03-18 [2] CRAN (R 3.6.1)
# crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
# curl 4.2 2019-09-24 [1] CRAN (R 3.6.1)
# digest 0.6.22 2019-10-21 [1] CRAN (R 3.6.1)
# dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
# ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
# glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
# gtable 0.3.0 2019-03-25 [2] CRAN (R 3.6.1)
# hms 0.5.2 2019-10-30 [1] CRAN (R 3.6.1)
# htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
# htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.1)
# httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
# jsonlite 1.6 2018-12-07 [2] CRAN (R 3.6.1)
# later 1.0.0 2019-10-04 [1] CRAN (R 3.6.1)
# lattice 0.20-38 2018-11-04 [3] CRAN (R 3.6.1)
# lazyeval 0.2.2 2019-03-15 [2] CRAN (R 3.6.1)
# lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
# lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.1)
# magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
# munsell 0.5.0 2018-06-12 [2] CRAN (R 3.6.1)
# pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
# png 0.1-7 2013-12-03 [2] CRAN (R 3.6.1)
# promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.1)
# pryr 0.1.4 2018-02-18 [2] CRAN (R 3.6.1)
# purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
# R6 2.4.0 2019-02-14 [2] CRAN (R 3.6.1)
# Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.1)
# readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
# remotes 2.1.0.9000 2019-09-26 [1] Github (MangoTheCat/remotes@2f1a040)
# rlang 0.4.1 2019-10-24 [1] CRAN (R 3.6.1)
# rmote * 0.3.4 2019-09-26 [1] Github (cloudyr/rmote@fbce611)
# scales 1.0.0 2018-08-09 [2] CRAN (R 3.6.1)
# servr 0.15 2019-08-07 [1] CRAN (R 3.6.1)
# sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
# sgejobs * 0.99.1 2019-11-07 [1] Github (LieberInstitute/sgejobs@f5ab0ca)
# stringi 1.4.3 2019-03-12 [2] CRAN (R 3.6.1)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
# tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
# tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
# tidyselect 0.2.5 2018-10-11 [2] CRAN (R 3.6.1)
# vctrs 0.2.0 2019-07-05 [1] CRAN (R 3.6.1)
# withr 2.1.2 2018-03-15 [2] CRAN (R 3.6.1)
# xfun 0.10 2019-10-01 [1] CRAN (R 3.6.1)
# zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
#
# [1] /users/lcollado/R/3.6
# [2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/site-library
# [3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-3.6/R/3.6/lib64/R/library
# >