pvanheus

  $ toil-cwl-runner --preserve-environment PATH --singularity ./example.cwl ./example-job.cwl 
/usr/people/pvh/miniconda3/envs/toil/lib/python2.7/site-packages/cwltool/__init__.py:17: CWLToolDeprecationWarning: 
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020.
Please upgrade your Python as the Python 2.7 version of cwltool won't be
maintained after that date.

  """,  category=CWLToolDeprecationWarning)
INFO:cwltool:Resolved './example.cwl' to 'file:///usr/people/pvh/toil/example.cwl'
WARNING:toil.batchSystems.singleMachine:Limiting maxCores to CPU count of system (24).
WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (33714651136).

pvanheus

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20191113
##source=freeBayes v1.3.1-dirty
##reference=reference/ref.fa
##contig=<ID=Chromosome,length=4411532>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-4411532"
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">

pvanheus

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20191113
##source=freeBayes v1.3.1-dirty
##reference=reference/ref.fa
##contig=<ID=Chromosome,length=4411532>
##phasing=none
##commandline="freebayes -p 2 -P 0 -C 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05 -f reference/ref.fa snps.bam --region Chromosome:0-4411532"
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">

pvanheus

DEBUG conda.gateways.logging:set_verbosity(231): verbosity set to 2
DEBUG conda.core.solve:solve_final_state(222): solving prefix /home/pvh/anaconda3/envs/rgi
  specs_to_remove: frozenset()
  specs_to_add: frozenset({MatchSpec("rgi")})
  prune: <auxlib._Null object at 0x7f64fad13ac8>
Collecting package metadata (current_repodata.json): ...working... DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True

pvanheus

DEBUG conda.gateways.logging:set_verbosity(231): verbosity set to 2
DEBUG conda.core.solve:solve_final_state(222): solving prefix /home/pvh/anaconda3/envs/rgi
  specs_to_remove: frozenset()
  specs_to_add: frozenset({MatchSpec("rgi=5.1.0")})
  prune: <auxlib._Null object at 0x7f2630af0a20>
Collecting package metadata (current_repodata.json): ...working... DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True
DEBUG conda.core.package_cache_data:_check_writable(259): package cache directory '/home/pvh/anaconda3/pkgs' writable: True

pvanheus

  (MTB_anc:0.0000404279,(ERR552627:0.0000095331,((ERR552650:0.0000037342,((((((((((((((ERR552714:0.0000016579,(ERR552408:0.0000008225,ERR552184:0.0000007560)93:0.000000231)90:0.000000696,(((ERR553080:0.0000045365,((ERR552633:0.0000026571,(ERR552243:0.0000018134,ERR553326:0.0000013601)100:0.000001425)95:0.000000683,ERR551209:0.0000031228)98:0.000000753)96:0.000001007,ERR552360:0.0000014937)84:0.000000755,ERR552967:0.0000011968)97:0.000001811)80:0.000000301,ERR552867:0.0000028514)85:0.000000749,ERR552368:0.0000020435)92:0.000000933,(((((((ERR551425:0.0000015400,(((ERR553305:0.0000015318,((ERR550804:0.0000020422,ERR552380:0.0000002294)86:0.000000694,ERR551517:0.0000015567)69:0.000000289)87:0.000000458,ERR551049:0.0000013181)91:0.000000926,ERR553279:0.0000002522)80:0.000000440)75:0.000000492,(((((ERR553288:0.0000011334,ERR551021:0.0000009067)98:0.000000774,((((((((((ERR552854:0.0000005301,ERR550691:0.0000019543)98:0.000000680,ERR552629:0.0000017437)100:0.000001673,(ERR553115:0.0000011389,(ERR551913:0.0000004540,E

pvanheus

>MTB_anc foo
CCCCGGGAGCCCGGTAGGCCGTCGGATGCGTCCCGCCCGGCGCGCCGTCCGCCACTCGGT
CGCACGCCCGGCCGGCCCCTAATGTTCGGCCACACCGAGCGGGCGAGAGGGGTGACTCGG
AGTCCCGGAGGCCGCCCCGGCCGAGTGCGTCGCCCACGCCGCGGCTTCCATGTGACATGC
TGGCCGAGCAGACAGAAGACGGGACGATCGCCCTCACGCGCGGGGGACCCGTGTGCAGGT
CCGGGGCCCGCAAGGCGACATGCCAACGGGCTTACACCCAATCTCCGCTGCTGTCCGCCA
ACACACGGTATTCCCCGGCGCGCCAGCCACGGGCTCTGGAGAACACCCATGACGGGGCGC
CCCGGCGCCCCCCCACGGAGAGGTACCGCCGCGGGAGCTCAGGGGGGCAGTTCTGGCCCT
ACGGAGGGCGGCTGTAGCCCGCCCTCTGCCCGAGCGGAGTCTCGGGGGCGGCGGGGACCT
CCGGATGCGTCTCTGAGGAGGTCTCGCGCCGCGTAGTTTGGTCTCAGCGCGACTGCGCCC

pvanheus

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: CommandLineTool
id: kraken2
baseCommand:
  - kraken2
inputs:
  database:
    type: 
      - Directory

pvanheus

library(tidyverse)
surveys <- read_csv("data_raw/portal_data_joined.csv")
str(surveys)

select(surveys, plot_id, species_id, weight)
select(surveys, -record_id, -species_id)

filter(surveys, year == 1995)

surveys2 <- filter(surveys, weight < 5)

pvanheus

download.file(url = "https://ndownloader.figshare.com/files/2292169",
              destfile = "data_raw/portal_data_joined.csv")

getwd()  # show where I am

surveys <- read.csv("data_raw/portal_data_joined.csv")

head(surveys)
View(surveys)
weight_g <- c(10, 50, 30)