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Copy pathSRP058181_leafcutter_ds.log
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SRP058181_leafcutter_ds.log
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nohup: ignoring input
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 3.2.1 v purrr 0.3.2
v tibble 2.1.3 v dplyr 0.8.3
v tidyr 1.0.0 v stringr 1.4.0
v readr 1.3.1 v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag() masks stats::lag()
[1] "Performing leafcutter differential splicing using the group file entitled: Control_vs_PDD"
Loading required package: Rcpp
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/intron_clustering/test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing/group_files//Control_vs_PDD_group_file.txt
Encoding as Control =0, PDD =1
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Settings:
$output_prefix
[1] "/home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing//Control_vs_PDD"
$max_cluster_size
[1] Inf
$min_samples_per_intron
[1] 5
$min_samples_per_group
[1] 3
$min_coverage
[1] 20
$timeout
[1] 30
$num_threads
[1] 15
$exon_file
[1] "/data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz"
$init
[1] "smart"
$seed
[1] 12345
$help
[1] FALSE
Running differential splicing analysis...
Differential splicing summary:
statuses Freq
1 <2 introns used in >=min_samples_per_intron samples 23
2 <=1 sample with coverage>0 4
3 <=1 sample with coverage>min_coverage 5362
4 Not enough valid samples 7293
5 Success 24339
Saving results...
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz
All done, exiting
[1] "Performing leafcutter differential splicing using the group file entitled: Control_vs_PD"
Loading required package: Rcpp
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/intron_clustering/test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing/group_files//Control_vs_PD_group_file.txt
Encoding as Control =0, PD =1
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Settings:
$output_prefix
[1] "/home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing//Control_vs_PD"
$max_cluster_size
[1] Inf
$min_samples_per_intron
[1] 5
$min_samples_per_group
[1] 3
$min_coverage
[1] 20
$timeout
[1] 30
$num_threads
[1] 15
$exon_file
[1] "/data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz"
$init
[1] "smart"
$seed
[1] 12345
$help
[1] FALSE
Running differential splicing analysis...
Differential splicing summary:
statuses Freq
1 <2 introns used in >=min_samples_per_intron samples 17
2 <=1 sample with coverage>0 3
3 <=1 sample with coverage>min_coverage 5364
4 Not enough valid samples 5306
5 Success 26330
6 timeout 1
Saving results...
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz
All done, exiting
[1] "Performing leafcutter differential splicing using the group file entitled: PD_vs_PDD"
Loading required package: Rcpp
Registered S3 method overwritten by 'R.oo':
method from
throw.default R.methodsS3
Loading counts from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/intron_clustering/test_diseasegroups_perind_numers.counts.gz
Loading metadata from /home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing/group_files//PD_vs_PDD_group_file.txt
Encoding as PD =0, PDD =1
Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Settings:
$output_prefix
[1] "/home/rreynolds/projects/Aim2_PDsequencing_wd/results/SRP058181/leafcutter/diff_splicing//PD_vs_PDD"
$max_cluster_size
[1] Inf
$min_samples_per_intron
[1] 5
$min_samples_per_group
[1] 3
$min_coverage
[1] 20
$timeout
[1] 30
$num_threads
[1] 15
$exon_file
[1] "/data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz"
$init
[1] "smart"
$seed
[1] 12345
$help
[1] FALSE
Running differential splicing analysis...
Differential splicing summary:
statuses Freq
1 <2 introns used in >=min_samples_per_intron samples 463
2 <=1 sample with coverage>0 9
3 <=1 sample with coverage>min_coverage 8353
4 Not enough valid samples 4385
5 Success 23811
Saving results...
Loading exons from /data/references/ensembl/gtf_gff3/v97/leafcutter/Homo_sapiens.GRCh38.97_LC_exon_file.txt.gz
All done, exiting