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PD_tissue_polyA_leafviz_PCaxes_prepare_results.log
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PD_tissue_polyA_leafviz_PCaxes_prepare_results.log
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nohup: ignoring input
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.2 v purrr 0.3.4
v tibble 3.0.3 v dplyr 1.0.2
v tidyr 1.1.1 v stringr 1.4.0
v readr 1.3.1 v forcats 0.5.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
[1] "Performing leafviz prepare_results for: Control_vs_DLB"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//Control_vs_DLB.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//Control_vs_DLB_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"
[1] "Performing leafviz prepare_results for: Control_vs_PDD"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//Control_vs_PDD.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//Control_vs_PDD_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"
[1] "Performing leafviz prepare_results for: Control_vs_PD"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//Control_vs_PD.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//Control_vs_PD_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"
[1] "Performing leafviz prepare_results for: PDD_vs_DLB"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//PDD_vs_DLB.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//PDD_vs_DLB_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"
[1] "Performing leafviz prepare_results for: PD_vs_DLB"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//PD_vs_DLB.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//PD_vs_DLB_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"
[1] "Performing leafviz prepare_results for: PD_vs_PDD"
Loading required package: leafcutter
Loading required package: Rcpp
Attaching package: 'dplyr'
The following objects are masked from 'package:data.table':
between, first, last
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Preparing for visualisation
Results to be saved in: /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/leafviz_PCaxes//PD_vs_PDD.Rda
Using annotation at: /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/intron_clustering/tissue_polyA_test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/leafcutter/diff_splicing_PCaxes/group_files//PD_vs_PDD_group_file.txt
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz
Taking input= as a system command ('zless /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_exons.txt.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_all_introns.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_threeprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
Taking input= as a system command ('zcat < /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_fiveprime.bed.gz') and a variable has been used in the expression passed to `input=`. Please use fread(cmd=...). There is a security concern if you are creating an app, and the app could have a malicious user, and the app is not running in a secure environment; e.g. the app is running as root. Please read item 5 in the NEWS file for v1.11.6 for more information and for the option to suppress this message.
[1] "Annotating junctions"
[1] "Preparing results"
[1] "converting counts to ratios"
`mutate_all()` ignored the following grouping variables:
Column `clu`
Use `mutate_at(df, vars(-group_cols()), myoperation)` to silence the message.
Warning message:
`funs()` is deprecated as of dplyr 0.8.0.
Please use a list of either functions or lambdas:
# Simple named list:
list(mean = mean, median = median)
# Auto named with `tibble::lst()`:
tibble::lst(mean, median)
# Using lambdas
list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
[1] "creating PCA"