shashidhar22 / nest Goto Github PK
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Home Page: https://shashidhar22.github.io/NeST/
I've installed NeST and the test run works. Now, I'm trying to run NeST on some CDC data which is publicly available (SRR7853847) and which I downloaded from SRA, but it's failing on prepInputs.
python3 ~/programs/NeST/nest.py -i public_data/fastqs/ -o public_data/output/ -a ~/programs/NeST/ref/pfalciparum/adapters.fa -r ~/programs/NeST/ref/pfalciparum/mdr.fa -b ~/programs/NeST/ref/pfalciparum/mdr.bed -m bowtie2 --varofint ref/pfalciparum/Reportable_SNPs.csv
2019-01-22 04:01:27,707 - NeST - INFO - Gathering input information from input path.
2019-01-22 04:01:27,712 - NeST.prepInputs - WARNING - Read from /home/ubuntu/public_data/fastqs/SRR7853847_2.fastq with header : @SRR7853847.1 1/2 does not follow any defined fastq header format.Please correct it
Traceback (most recent call last):
File "/home/ubuntu/programs/NeST/nest.py", line 451, in <module>
args.pic_path, args.voi_path, java_def, sra_def, args.verbose)
File "/home/ubuntu/programs/NeST/nest.py", line 348, in marsBatch
config = prep.prepInputs()
File "/home/ubuntu/programs/NeST/nest/prepinputs.py", line 304, in prepInputs
experiment[sample] = Sample(sample, lib, seqType,
UnboundLocalError: local variable 'lib' referenced before assignment
From a comparison of fastq headers of the working sample and the failing sample, I would guess that it is having a problem with the slash in the header?
Working:
@SRR6463548.1 1 length=65
Failing:
@SRR7853847.1 1/2
Hello, me again! :-)
I'm testing NeST with some data from SRA but it's failing to run NovelExonicNonSynSNPs.R
Terminal output is below:
(nest) ubuntu@nhien-malaria:~$ python3 ~/programs/NeST/nest.py -i public_data/fastqs/ -a programs/NeST/ref/pfalciparum/adapters.fa -r programs/NeST/ref/pfalciparum/mdr.fa -o public_data/output/ -b programs/NeST/ref/pfalciparum/mdr.bed -m bowtie2 --varofint programs/NeST/ref/pfalciparum/Reportable_SNPs.csv
2019-01-25 06:43:10,348 - NeST - INFO - Gathering input information from input path.
2019-01-25 06:43:10,361 - NeST.prepInputs - INFO - A total of 1 libraries were identified from the given folder /home/ubuntu/public_data/fastqs
2019-01-25 06:43:10,361 - NeST - INFO - Running MaRS on 1 experiments
2019-01-25 06:43:21,007 - NeST.SRR7853847 - INFO - Total variants : 5; Verified calls : 5; Exonic : 5; Intronic : 0; Synonymous : 1; Non Synonymous : 4; Transition : 2; Transversion : 3
2019-01-25 06:43:21,008 - NeST - INFO - Summarizing variant calls from all 1 experiments
2019-01-25 06:43:21,942 - NeST.Summary - INFO - Plotting Depth Per SNP
2019-01-25 06:43:28,986 - NeST.Summary - INFO - Plotting Reportable SNPs Frequency
2019-01-25 06:43:30,239 - NeST.Summary - INFO - Plotting Novel Exonic Non-Synonymous SNPs
2019-01-25 06:43:31,555 - NeST.Summary - ERROR - Failed to execute NovelExonicNonSynSNPs.R
2019-01-25 06:43:31,556 - NeST.Summary - ERROR - Rscript /home/ubuntu/programs/NeST/nest/Rscripts/NovelExonicNonSynSNPs.R -i public_data/output//Reports/Study_novel_exonic_variants.csv -o public_data/output//Figures/
2019-01-25 06:43:31,556 - NeST.Summary - INFO - Plotting Novel Exonic Synonymous SNPs
2019-01-25 06:43:32,985 - NeST.Summary - ERROR - Failed to execute NovelExonicSynSNPs.R
2019-01-25 06:43:32,986 - NeST.Summary - ERROR - Rscript /home/ubuntu/programs/NeST/nest/Rscripts/reportableSNPsFreq.R -i public_data/output//Reports/Study_known_variants.csv -r programs/NeST/ref/pfalciparum/Reportable_SNPs.csv -o public_data/output//Figures/
2019-01-25 06:43:32,986 - NeST.Summary - INFO - Plotting Novel Intronic SNPs
2019-01-25 06:43:33,818 - NeST.Summary - ERROR - Failed to execute NovelIntronicSNPs.R
2019-01-25 06:43:33,818 - NeST.Summary - ERROR - Rscript /home/ubuntu/programs/NeST/nest/Rscripts/NovelIntronicSNPs.R -i public_data/output//Reports/Study_novel_intronic_variants.csv -o public_data/output//Figures/
Traceback (most recent call last):
File "/home/ubuntu/programs/NeST/nest.py", line 451, in <module>
args.pic_path, args.voi_path, java_def, sra_def, args.verbose)
File "/home/ubuntu/programs/NeST/nest.py", line 373, in marsBatch
summary.getSummary()
File "/home/ubuntu/programs/NeST/nest/summarize.py", line 753, in getSummary
os.remove('{0}/novel_SNPs_intronic.csv'.format(fig_path))
FileNotFoundError: [Errno 2] No such file or directory: 'public_data/output//Figures/novel_SNPs_intronic.csv'
When I try to run the Rscript just by itself, I get this output
(nest) ubuntu@nhien-malaria:~$ Rscript /home/ubuntu/programs/NeST/nest/Rscripts/NovelExonicNonSynSNPs.R -i public_data/output/Reports/Study_novel_exonic_variants.csv -o public_data/output/Figures/
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Parsed with column specification:
cols(
Sample = col_character(),
Variant = col_character(),
Chrom = col_character(),
Gene = col_character(),
Ref = col_character(),
Alt = col_logical(),
Pos = col_integer(),
Qual = col_double(),
RefCodon = col_character(),
RefAA = col_character(),
AltCodon = col_character(),
AltAA = col_character(),
AAPos = col_integer(),
Exon = col_character(),
AF = col_double(),
DP = col_integer(),
Conf = col_integer()
)
Parsed with column specification:
cols(
Sample = col_character(),
Variant = col_character(),
Chrom = col_character(),
Gene = col_character(),
Ref = col_character(),
Alt = col_logical(),
Pos = col_integer(),
Qual = col_double(),
RefCodon = col_character(),
RefAA = col_character(),
AltCodon = col_character(),
AltAA = col_character(),
AAPos = col_integer(),
Exon = col_character(),
AF = col_integer(),
DP = col_integer(),
Conf = col_integer()
)
Parsed with column specification:
cols(
gene = col_character(),
`AAPos=` = col_character(),
`RefAA=` = col_character(),
`AltAA=` = col_character(),
name = col_character()
)
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 1
Calls: cbind -> cbind -> data.frame
Execution halted
Just in case it's useful, here are the files which NeST makes in the output dir
(nest) ubuntu@nhien-malaria:~$ tree public_data/output/
├── Figures
│ ├── novel_SNPs_exonic_nonsyn.csv
│ ├── Novel_SNPs_exonic_syn.pdf
│ ├── Novel_SNPs_Report_exonic_syn.csv
│ ├── Reportable_SNPs.pdf
│ ├── Reportable_SNPs_Report.csv
│ ├── Study_depth.pdf
│ └── Study_novel_exonic_variants_filtered.csv
├── nest.log
├── Reports
│ ├── Study_known_variants_allele_frequency.csv
│ ├── Study_known_variants.csv
│ ├── Study_known_variants_depth.csv
│ ├── Study_novel_exonic_variants.csv
│ ├── Study_novel_variants_allele_frequency.csv
│ └── Study_novel_variants_depth.csv
├── SRR7853847
│ ├── alignments
│ │ ├── output_FM.bam
│ │ ├── output_FM_SR.bam
│ │ ├── output_FM_SR_DD.bam
│ │ ├── output_FM_SR_DD_RG.bai
│ │ ├── output_FM_SR_DD_RG.bam
│ │ └── output.sam
│ ├── CleanedFastq
│ │ ├── SRR7853847_1.fastq_cleaned.fq
│ │ ├── SRR7853847_2.fastq_cleaned.fq
│ │ └── SRR7853847_2.fastq_stats.txt
│ ├── completion
│ │ ├── align.rt
│ │ ├── bbduk.rt
│ │ ├── bcfcall.rt
│ │ ├── bcfindex.rt
│ │ ├── dedup.rt
│ │ ├── fixmate.rt
│ │ ├── gatk.rt
│ │ ├── pileup.rt
│ │ ├── readgroup.rt
│ │ └── sort.rt
│ ├── mod_fasta.fa
│ ├── SRR7853847_variants.bcf
│ ├── SRR7853847_variants.bcf.csi
│ ├── SRR7853847_variants_gatk_annotated.vcf
│ ├── SRR7853847_variants_gatk.vcf
│ ├── SRR7853847_variants_gatk.vcf.idx
│ ├── SRR7853847_variants_merged_annotated.vcf
│ ├── SRR7853847_variants_samtools_annotated.vcf
│ └── SRR7853847_variants_samtools.vcf
└── Study_variants.json
And their sizes
(nest) ubuntu@nhien-malaria:~$ ls -lh public_data/output/*/*
-rw-rw-r-- 1 ubuntu ubuntu 31 Jan 25 06:49 public_data/output/Figures/novel_SNPs_exonic_nonsyn.csv
-rw-rw-r-- 1 ubuntu ubuntu 3.6K Jan 25 06:44 public_data/output/Figures/Novel_SNPs_exonic_syn.pdf
-rw-rw-r-- 1 ubuntu ubuntu 129 Jan 25 06:44 public_data/output/Figures/Novel_SNPs_Report_exonic_syn.csv
-rw-rw-r-- 1 ubuntu ubuntu 5.7K Jan 25 06:44 public_data/output/Figures/Reportable_SNPs.pdf
-rw-rw-r-- 1 ubuntu ubuntu 2.9K Jan 25 06:44 public_data/output/Figures/Reportable_SNPs_Report.csv
-rw-rw-r-- 1 ubuntu ubuntu 8.2K Jan 25 06:44 public_data/output/Figures/Study_depth.pdf
-rw-rw-r-- 1 ubuntu ubuntu 183 Jan 25 06:49 public_data/output/Figures/Study_novel_exonic_variants_filtered.csv
-rw-rw-r-- 1 ubuntu ubuntu 727 Jan 25 06:43 public_data/output/Reports/Study_known_variants_allele_frequency.csv
-rw-rw-r-- 1 ubuntu ubuntu 3.8K Jan 25 06:43 public_data/output/Reports/Study_known_variants.csv
-rw-rw-r-- 1 ubuntu ubuntu 787 Jan 25 06:43 public_data/output/Reports/Study_known_variants_depth.csv
-rw-rw-r-- 1 ubuntu ubuntu 182 Jan 25 06:43 public_data/output/Reports/Study_novel_exonic_variants.csv
-rw-rw-r-- 1 ubuntu ubuntu 38 Jan 25 06:43 public_data/output/Reports/Study_novel_variants_allele_frequency.csv
-rw-rw-r-- 1 ubuntu ubuntu 35 Jan 25 06:43 public_data/output/Reports/Study_novel_variants_depth.csv
-rw-rw-r-- 1 ubuntu ubuntu 20K Jan 25 06:43 public_data/output/SRR7853847/mod_fasta.fa
-rw-rw-r-- 1 ubuntu ubuntu 90K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants.bcf
-rw-rw-r-- 1 ubuntu ubuntu 182 Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants.bcf.csi
-rw-rw-r-- 1 ubuntu ubuntu 9.9K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_gatk_annotated.vcf
-rw-rw-r-- 1 ubuntu ubuntu 8.2K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_gatk.vcf
-rw-rw-r-- 1 ubuntu ubuntu 395 Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_gatk.vcf.idx
-rw-rw-r-- 1 ubuntu ubuntu 12K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_merged_annotated.vcf
-rw-rw-r-- 1 ubuntu ubuntu 5.2K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_samtools_annotated.vcf
-rw-rw-r-- 1 ubuntu ubuntu 3.5K Jan 25 06:43 public_data/output/SRR7853847/SRR7853847_variants_samtools.vcf
public_data/output/SRR7853847/alignments:
total 7.2M
-rw-rw-r-- 1 ubuntu ubuntu 931K Jan 25 06:43 output_FM.bam
-rw-rw-r-- 1 ubuntu ubuntu 907K Jan 25 06:43 output_FM_SR.bam
-rw-rw-r-- 1 ubuntu ubuntu 906K Jan 25 06:43 output_FM_SR_DD.bam
-rw-rw-r-- 1 ubuntu ubuntu 496 Jan 25 06:43 output_FM_SR_DD_RG.bai
-rw-rw-r-- 1 ubuntu ubuntu 899K Jan 25 06:43 output_FM_SR_DD_RG.bam
-rw-rw-r-- 1 ubuntu ubuntu 3.6M Jan 25 06:43 output.sam
public_data/output/SRR7853847/CleanedFastq:
total 3.5M
-rw-rw-r-- 1 ubuntu ubuntu 1.9M Jan 25 06:43 SRR7853847_1.fastq_cleaned.fq
-rw-rw-r-- 1 ubuntu ubuntu 1.7M Jan 25 06:43 SRR7853847_2.fastq_cleaned.fq
-rw-rw-r-- 1 ubuntu ubuntu 254 Jan 25 06:43 SRR7853847_2.fastq_stats.txt
public_data/output/SRR7853847/completion:
total 0
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 align.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 bbduk.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 bcfcall.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 bcfindex.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 dedup.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 fixmate.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 gatk.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 pileup.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 readgroup.rt
-rw-rw-r-- 1 ubuntu ubuntu 0 Jan 25 06:43 sort.rt
Hello,
I'm trying to get NeST up and running on Ubuntu 14.04, i have already installed conda, but NeST is not installing.
ubuntu@ashton-oucru-1:~/programs/NeST$ conda env create -n nest -f lib/nest_env.yaml
Using Anaconda Cloud api site https://api.anaconda.org
Solving environment: failed
ResolvePackageNotFound:
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-cli
- r-crayon
- r-base=3.3.2
- _r-mutex=1[build=anacondar_1]
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-cli
- r-assertthat
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-rlang
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-pillar[version='>=1.1.0']
- r-utf8[version='>=1.1.3']
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-pillar[version='>=1.1.0']
- r-fansi
- r-dplyr=0.7.6
- r-tibble[version='>=1.3.1']
- r-rcpp[version='>=0.12.3']
- r-dplyr=0.7.6
- r-tidyselect[version='>=0.2.3']
- r-purrr
- r-lazyeval[version='>=0.2.0']
- r-dplyr=0.7.6
- r-tidyselect[version='>=0.2.3']
- r-purrr
- r-bh
- r=3.3.1
- r-dplyr=0.7.6
- r-tidyselect[version='>=0.2.3']
- r-purrr
- r-magrittr[version='>=1.5']
- r-dplyr=0.7.6
- r-tidyselect[version='>=0.2.3']
- r-glue
- r-dplyr=0.7.6
- r-pkgconfig[version='>=2.0.1']
- r-dplyr=0.7.6
- r-plogr[version='>=0.1.10']
- r-dplyr=0.7.6
- r-bindrcpp[version='>=0.2.0.9000']
- r-bindr[version='>=0.1.1']
- r-dplyr=0.7.6
- r-r6[version='>=2.2.2']
- r-stringr=1.3.1
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-stringr=1.3.1
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-stringr=1.3.1
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-stringr=1.3.1
- r-stringi[version='>=1.1.7']
- r-stringr=1.3.1
- r-magrittr
- r=3.2.2
- r-stringr=1.3.1
- r-glue[version='>=1.2.0']
- r-rcolorbrewer=1.1_2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-rcolorbrewer=1.1_2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-rcolorbrewer=1.1_2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-tidyr=0.8.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-tidyr=0.8.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-tidyr=0.8.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-tidyr=0.8.1
- r-tibble
- r-rcpp
- r-tidyr=0.8.1
- r-tibble
- r-assertthat
- r-tidyr=0.8.1
- r-tibble
- r-cli
- r-crayon
- r-tidyr=0.8.1
- r-tibble
- r-rlang
- r-tidyr=0.8.1
- r-tibble
- r-pillar[version='>=1.1.0']
- r-utf8[version='>=1.1.3']
- r-tidyr=0.8.1
- r-tibble
- r-pillar[version='>=1.1.0']
- r-fansi
- r-tidyr=0.8.1
- r-stringi
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-bh
- r=3.3.1
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-r6
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-dbi[version='>=0.4.1']
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-magrittr
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-pkgconfig[version='>=2.0.1']
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-plogr[version='>=0.1.10']
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-bindrcpp[version='>=0.2.0.9000']
- r-bindr[version='>=0.1.1']
- r-tidyr=0.8.1
- r-tidyselect
- r-purrr
- r-dplyr
- r-glue[version='>=1.1.1']
- r=3.4.1
- r-base==3.4.1
- _r-mutex=1[build=anacondar_1]
- r=3.4.1
- r-recommended==3.4.1
- r-matrix
- r-lattice
- r=3.4.1
- r-recommended==3.4.1
- r-cluster
- r=3.4.1
- r-recommended==3.4.1
- r-survival
- r=3.4.1
- r-recommended==3.4.1
- r-nnet
- r=3.4.1
- r-recommended==3.4.1
- r-kernsmooth
- r=3.4.1
- r-recommended==3.4.1
- r-codetools
- r=3.4.1
- r-recommended==3.4.1
- r-foreign
- r=3.4.1
- r-recommended==3.4.1
- r-class
- r-mass
- r=3.4.1
- r-recommended==3.4.1
- r-spatial
- r=3.4.1
- r-recommended==3.4.1
- r-boot
- r=3.4.1
- r-recommended==3.4.1
- r-rpart
- r=3.4.1
- r-recommended==3.4.1
- r-nlme
- r=3.4.1
- r-recommended==3.4.1
- r-mgcv
- r-getopt=1.20.2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-getopt=1.20.2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-getopt=1.20.2
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-ggplot2=3.0.0
- r-withr[version='>=2.0.0']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-ggplot2=3.0.0
- r-withr[version='>=2.0.0']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-ggplot2=3.0.0
- r-withr[version='>=2.0.0']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-ggplot2=3.0.0
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-ggplot2=3.0.0
- r-tibble
- r-rcpp
- r-ggplot2=3.0.0
- r-tibble
- r-assertthat
- r-ggplot2=3.0.0
- r-tibble
- r-cli
- r-crayon
- r-ggplot2=3.0.0
- r-tibble
- r-rlang
- r-ggplot2=3.0.0
- r-tibble
- r-pillar[version='>=1.1.0']
- r-utf8[version='>=1.1.3']
- r-ggplot2=3.0.0
- r-tibble
- r-pillar[version='>=1.1.0']
- r-fansi
- r-ggplot2=3.0.0
- r-mass
- r-ggplot2=3.0.0
- r-plyr[version='>=1.7.1']
- r-ggplot2=3.0.0
- r-gtable[version='>=0.1.1']
- r-ggplot2=3.0.0
- r-viridislite
- r-ggplot2=3.0.0
- r-reshape2
- r-stringr
- r-stringi[version='>=1.1.6']
- r-ggplot2=3.0.0
- r-reshape2
- r-stringr
- r-magrittr
- r=3.2.2
- r-ggplot2=3.0.0
- r-reshape2
- r-stringr
- r-glue
- r-ggplot2=3.0.0
- r-scales[version='>=0.5.0']
- r-rcolorbrewer
- r-ggplot2=3.0.0
- r-scales[version='>=0.5.0']
- r-labeling
- r-ggplot2=3.0.0
- r-scales[version='>=0.5.0']
- r-munsell[version='>=0.2']
- r-colorspace
- r-ggplot2=3.0.0
- r-scales[version='>=0.5.0']
- r-r6
- r-ggplot2=3.0.0
- r-scales[version='>=0.5.0']
- r-dichromat
- r-ggplot2=3.0.0
- r-digest
- r-ggplot2=3.0.0
- r-mgcv
- r-matrix
- r-lattice
- r-ggplot2=3.0.0
- r-mgcv
- r-nlme[version='>=3.1_64']
- r-optparse=1.6.0
- r-getopt[version='>=1.20.2']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-optparse=1.6.0
- r-getopt[version='>=1.20.2']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-optparse=1.6.0
- r-getopt[version='>=1.20.2']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-readr=1.1.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- _r-mutex=1[build=anacondar_1]
- r-readr=1.1.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- tktable
- r-readr=1.1.1
- r-tibble
- r-lazyeval[version='>=0.1.10']
- r-base[version='>=3.5.1,<3.5.2.0a0']
- bwidget
- r-readr=1.1.1
- r-tibble
- r-rcpp
- r-readr=1.1.1
- r-tibble
- r-assertthat
- r-readr=1.1.1
- r-tibble
- r-cli
- r-crayon
- r-readr=1.1.1
- r-tibble
- r-rlang
- r-readr=1.1.1
- r-tibble
- r-pillar[version='>=1.1.0']
- r-utf8[version='>=1.1.3']
- r-readr=1.1.1
- r-tibble
- r-pillar[version='>=1.1.0']
- r-fansi
- r-readr=1.1.1
- r-hms
- r-pkgconfig
- r-readr=1.1.1
- r-bh
- r=3.3.1
- r-readr=1.1.1
- r-r6
Below is the output of the conda info
command.
active environment : None
user config file : /home/ubuntu/.condarc
populated config files : /home/ubuntu/.condarc
conda version : 4.5.11
conda-build version : 1.21.3
python version : 2.7.12.final.0
base environment : /home/ubuntu/anaconda2 (writable)
channel URLs : https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/pro/linux-64
https://repo.anaconda.com/pkgs/pro/noarch
package cache : /home/ubuntu/anaconda2/pkgs
/home/ubuntu/.conda/pkgs
envs directories : /home/ubuntu/anaconda2/envs
/home/ubuntu/.conda/envs
platform : linux-64
user-agent : conda/4.5.11 requests/2.14.2 CPython/2.7.12 Linux/3.13.0-88-generic ubuntu/14.04 glibc/2.19
UID:GID : 1000:1000
netrc file : None
offline mode : False
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