CalledProcessError in line 28 of /home/imp/code/rules/Analysis/visualize_mg.rules
Encountered an error in the visualize
rule:
rule visualize:
input: Analysis/mg.read_counts.txt, Analysis/mg.assembly.contig_flagstat.txt, Analysis/mg.assembly.contig_coverage.txt, Analysis/mg.as
sembly.contig_depth.txt, Analysis/mg.variants.samtools.vcf.gz, Analysis/mg.assembly.gc_content.txt, Analysis/annotation/annotation.filt.gff, A
nalysis/mg.vizbin.with-contig-names.points, Analysis/results/quast/summary/combined_quast_output/contigs_reports/nucmer_output/aux/mg.assembly.merged.coords_edited
output: Analysis/results/IMP-vizbin_length.png, Analysis/results/IMP-vizbin_length_GC.png, Analysis/results/IMP-vizbin_standard.png, Analysis/results/IMP-mg_var_count.png, Analysis/results/IMP-mg_coverage_density.png, Analysis/results/IMP-mg_reads_density.png, Analysis/results/IMP-mg_vizbin_length_cov.png, Analysis/results/IMP-mg_vizbin_length_depth.png, Analysis/results/IMP-mg_vizbin_length_vardens.png, Analysis/results/mg.read_stats.html, Analysis/results/mg.read_stats.txt, Analysis/results/mg_mapping_stats.html, Analysis/results/mg_mapping_stats.txt, Analysis/results/mg_results.Rdat
[x] PLOT 2018/02/13 21:23:09
[1] "Loading required R libraries"
Loading required package: genomeIntervals
Loading required package: methods
Loading required package: intervals
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Loading required package: checkpoint
checkpoint: Part of the Reproducible R Toolkit from Microsoft
https://mran.microsoft.com/documents/rro/reproducibility/
checkpoint process complete
---
Loading required package: ggplot2
Loading required package: gtools
Loading required package: data.table
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'data.table'
Loading required package: reshape
Attaching package: 'reshape'
The following object is masked from 'package:intervals':
expand
Loading required package: grid
Loading required package: stringr
Loading required package: xtable
Loading required package: beanplot
Loading required package: psych
Attaching package: 'psych'
The following object is masked from 'package:gtools':
logit
The following objects are masked from 'package:ggplot2':
%+%, alpha
[1] "START: Reading arguments"
[1] "DONE: Reading arguments"
[1] "START: Reading functions"
[1] "DONE: Reading functions"
[1] "Reading input files..."
[1] "Read in MG read count file"
[1] "Read in MG mapping summary file"
[1] "Read in MG coverage file"
[1] "Read in MG depth file"
[1] "Read in MG variant calls"
[1] "Read in GC percentage file"
[1] "Read in gff3 annotation file"
Read 244021 records
Error in validObject(.Object) :
invalid class "Genome_intervals_stranded" object: The 'annotation' slot should have a column named 'inter_base' that is logical and does not contain missing values.
Calls: readGff3 ... eval -> eval -> .nextMethod -> initMatrix -> validObject
In addition: Warning message:
In readGff3(annot_file, isRightOpen = T) :
'readGff3' has changed to closed interval conventions!
Use 'isRightOpen=TRUE' to restore the previous behavior
that allowed for zero-length features. Alternatively, use
the readZeroLengthFeaturesGff3 function instead.
You can turn off this warning by setting 'quiet=TRUE'
Execution halted
Error in job visualize while creating output files Analysis/results/IMP-vizbin_length.png, Analysis/results/IMP-vizbin_length_GC.png, Analysis/results/IMP-vizbin_standard.png, Analysis/results/IMP-mg_var_count.png, Analysis/results/IMP-mg_coverage_density.png, Analysis/results/IMP-mg_reads_density.png, Analysis/results/IMP-mg_vizbin_length_cov.png, Analysis/results/IMP-mg_vizbin_length_depth.png, Analysis/results/IMP-mg_vizbin_length_vardens.png, Analysis/results/mg.read_stats.html, Analysis/results/mg.read_stats.txt, Analysis/results/mg_mapping_stats.html, Analysis/results/mg_mapping_stats.txt, Analysis/results/mg_results.Rdat.
RuleException:
CalledProcessError in line 28 of /home/imp/code/rules/Analysis/visualize_mg.rules:
Command '
PLOT_SCRIPT="/home/imp/code/src/IMP_visualize_mg.R"
echo "[x] PLOT `date +"%Y/%m/%d %H:%M:%S"`"
mkdir -p Analysis/results
Rscript $PLOT_SCRIPT Analysis/results Analysis/mg.read_counts.txt Analysis/mg.assembly.contig_flagstat.txt Analysis/mg.assembly.contig_coverage.txt Analysis/mg.assembly.contig_depth.txt Analysis/mg.variants.samtools.vcf.gz Analysis/mg.assembly.gc_content.txt Analysis/annotation/annotation.filt.gff Analysis/mg.vizbin.with-contig-names.points Analysis/results/quast/summary/combined_quast_output/contigs_reports/nucmer_output/aux/mg.assembly.merged.coords_edited /home/imp/code/src/IMP_plot_functions.R
' returned non-zero exit status 1
File "/usr/lib/python3.4/concurrent/futures/thread.py", line 54, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
Any ideas on how to proceed from here?