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Home Page: https://shashidhar22.github.io/NeST/

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nest's Issues

FASTQ from SRA not parsed by 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

Problem with Rscript NovelExonicNonSynSNPs.R

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

Problem with following install instructions

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

NeST error : reports and figure folder is empty.

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