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Mon Feb 12 15:27:41 2018	Validating options...
Mon Feb 12 15:27:41 2018	Starting ☲☴ lncRNApipe Pipeline...
Mon Feb 12 15:27:41 2018	########################### Module 1: Running cuffcompare... #########################################

Making output directory for cuffcompare [ /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffcompare ]


Command call:
-------------
/usr/local/bin/cuffcompare -T -o /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffcompare/lncRNApipe_cuffcmp -r /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genes.gtf -s /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genome.fa /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.2cells/transcripts.gtf /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf 

Error: cannot locate input file: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf

INFO!!
--------
Using local FASTA reference [ genome.fa ] to fetch sequences to maintain consistency.
** Requires Bio::SeqIO module to be installed and available **


Mon Feb 12 15:27:41 2018	########################### Module 2: Running categorize_ncRNAs.pl ###################################

Cannot find Cuffcompare tracking [ /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffcompare/lncRNApipe_cuffcmp.tracking ] file...

ERROR

Mon Feb 12 15:27:41 2018	☲☴ lncRNApipe Pipeline aborted(?)



Mon Feb 12 15:27:41 2018	Validating options...

Mon Feb 12 15:27:41 2018	Starting ☲☴ lncRNApipe Pipeline...

Mon Feb 12 15:27:41 2018	########################### Module 1: Running cuffcompare... #########################################

Making output directory for cuffcompare [ /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_known_ncRNAs/cuffcompare ]


Command call:
-------------
/usr/local/bin/cuffcompare -T -o /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_known_ncRNAs/cuffcompare/lncRNApipe_cuffcmp -r /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/zf_noncode2016.gtf -s /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genome.fa /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.2cells/transcripts.gtf /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf 

Error: cannot locate input file: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf

INFO!!
--------
Using local FASTA reference [ genome.fa ] to fetch sequences to maintain consistency.
** Requires Bio::SeqIO module to be installed and available **


Mon Feb 12 15:27:41 2018	########################### Module 2: Running categorize_ncRNAs.pl ###################################

Cannot find Cuffcompare tracking [ /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_known_ncRNAs/cuffcompare/lncRNApipe_cuffcmp.tracking ] file...

ERROR
Mon Feb 12 15:27:41 2018	☲☴ lncRNApipe Pipeline aborted(?)

yeroslaviz@cotopaxi:lncRNApipe$ ll /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf
-rw-rw-r-- 1 yeroslaviz yeroslaviz 3588058 Feb 12 15:27 /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/transcripts.gtf

perl lncRNApipe --conf lncRNApipe-test/params.test.yaml

Mon Feb 12 15:54:13 2018        Validating options...

Mon Feb 12 15:54:13 2018        Starting ☲☴ lncRNApipe Pipeline...

Mon Feb 12 15:54:13 2018        Preparing output directories...

Mon Feb 12 15:54:13 2018        Creating a GTF file with gene_biotype which is not "protein_coding"...

WARNING!
--------
[performTranscriptAssembly: YES] requested, but found [cuffcompare: ] options.
[cuffcompare: ] options are not required when you are performing transcript assembly with lncRNApipe.


Mon Feb 12 15:54:13 2018        Preparing job scripts...

Mon Feb 12 15:54:13 2018        Detected PE / MP reads...

Mon Feb 12 15:54:13 2018        Job script [ lncRNApipe_alignment_stage_run_jJMDrZlC1UCY.2cells_rep_1.sh  ] written...

Mon Feb 12 15:54:13 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_alignment_stage_run_jJMDrZlC1UCY.2cells_rep_1.sh &


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Mon Feb 12 15:54:13 2018        Waiting for 1 more job ID(s) in [ job_IDs_tophat.jJMDrZlC1UCY ]...

Mon Feb 12 15:54:23 2018        Job script [ lncRNApipe_assembly_stage_run_jJMDrZlC1UCY.2cells.sh  ] written...

Mon Feb 12 15:54:23 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_assembly_stage_run_jJMDrZlC1UCY.2cells.sh &


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Mon Feb 12 15:54:23 2018        Job script [ lncRNApipe_alignment_stage_run_jJMDrZlC1UCY.6h_rep_1.sh  ] written...

Mon Feb 12 15:54:23 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_alignment_stage_run_jJMDrZlC1UCY.6h_rep_1.sh &


@ -------------------------------------------------------------------- @

Mon Feb 12 15:54:23 2018        Waiting for 1 more job ID(s) in [ job_IDs_tophat.jJMDrZlC1UCY ]...

Mon Feb 12 15:54:33 2018        Job script [ lncRNApipe_assembly_stage_run_jJMDrZlC1UCY.6h.sh  ] written...

Mon Feb 12 15:54:33 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_assembly_stage_run_jJMDrZlC1UCY.6h.sh &


@ -------------------------------------------------------------------- @

Mon Feb 12 15:54:33 2018        Waiting for 1 more job ID(s) in [ job_IDs_cufflinks.jJMDrZlC1UCY ]...

Mon Feb 12 15:54:43 2018        Job script [ lncRNApipe_postAssembly.run_jJMDrZlC1UCY.sh  ] written...

Mon Feb 12 15:54:43 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_postAssembly.run_jJMDrZlC1UCY.sh &


@ -------------------------------------------------------------------- @

Mon Feb 12 15:54:43 2018        cuffdiff run on all cufflinks' transcripts requested...

Mon Feb 12 15:54:43 2018        Generating separate job script using the same job dependency chain...

Mon Feb 12 15:54:43 2018        Job script [ lncRNApipe_postAssembly_diffExp.run_jJMDrZlC1UCY.sh  ] written...

Mon Feb 12 15:54:43 2018        No scheduler specified. Running it in background with bash...

@ -------------------------------------------------------------------- @

Command call:
-------------
bash /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/job_scripts.Mon_Feb_12_15_54_13_2018/lncRNApipe_postAssembly_diffExp.run_jJMDrZlC1UCY.sh &


@ -------------------------------------------------------------------- @

Mon Feb 12 15:54:43 2018        All job scripts have been submitted. Please check these log files for any results / errors.

/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/trimmomatic/run_jJMDrZlC1UCY.2cells_rep_1/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/tophat/run_jJMDrZlC1UCY.2cells_rep_1/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.2cells/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/trimmomatic/run_jJMDrZlC1UCY.6h_rep_1/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/tophat/run_jJMDrZlC1UCY.6h_rep_1/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cufflinks/run_jJMDrZlC1UCY.6h/run.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/lncRNApipe.postAssembly.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffmerge_known_ncRNAs/cuffmerge_known_ncRNAs.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffmerge_novel_ncRNAs/cuffmerge_novel_ncRNAs.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_known_ncRNAs/cuffdiff_on_known.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_novel_ncRNAs/cuffdiff_on_novel.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_on_transcripts/cuffmerge_on_cufflinks_transcripts.run_jJMDrZlC1UCY.log
/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run/cuffdiff_on_transcripts/cuffdiff_on_all_transcripts.run_jJMDrZlC1UCY.log

---
# This is the configuration file, where you can specify the command line
# options for each of the modules of lncRNApipe. If you do not wish to
# run any of the modules, simply, disable them and all the lines following
# it (if, any) by prefixing it with #
#
# 
#
# Specify output directory.
# In the example below, a  new output directory called "run"
# will be created at the mentioned path  /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test.
#
outputDir: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/run

#
# Indicate, if we should overwrite the output directory if it already exists.
#
# WARNING: THIS WILL REMOVE ANY FILES / DIRECTORIES 
#
overwriteOutputDir: NO

#
# Let lncRNApipe know if you intend to perform transcript assembly
# using tophat / cufflinks or just identify ncRNAs from already
# assembled transcripts.
#
performTranscriptAssembly: YES

#
# Specify number of threads / CPUs to use where possible.
# If running on a grid, each job script will run with this many
# number of CPUs.
#
# ********************* !! IMPORTANT !! ***********************
# *************************************************************
#
# Please be aware that each command will take this many number
# of CPUs. If you have 2 samples, then 2 tophat runs will take
# 10 CPUs each etc... In case of grid computing, this is easily
# managed via job parameters but if you not using grid computing, 
# please make sure you are not exceeding the total number of CPUs
# available on your machine. 
#
# For example, if you are not using grid computing and your  machine 
# has 24 CPUs, and you have 6 samples including all replicates, 
# you may want to use as rule of thumb: 
#
# Desired number of CPUs = Total number of CPUs divided by total
# number of samples (including replicates, if any)
# 
CPUs: 16

#
# Specify scheduler type.
# Valid options are PBS, SGE, LSF or NONE to disable grid computing.
#
#scheduler: SGE
scheduler: NONE

#
# Mention batch submission command.
# For example, for LSF, it is bsub, for PBS or SGE, it
# is qsub and in case you are not running jobs on the cluster, change
# it to BASH.
#
# batchSubCmd: qsub
batchSubCmd: BASH

#
# Specify scheduler options on separate line
# specific to your job running environment.
#
# ********************* !! IMPORTANT !! ***********************
# *************************************************************
#
# Different clusters uses different job parameter names. For
# example our cluster uses num_threads as parameter name to
# request number of CPUs in SGE. Some clusters may use
# num_cpu. Since it is difficult to guess, please provide
# number of CPUs you want to use based on your grid environment
# below, which is equal to "CPUs:" option above. Yes, we know that
# this is kind of redundant but it is necessary evil. What ever
# job parameters you provide after the - , they will appear
# exactly in the job script.
#
# IF IT IS NOT PROVIDED, THE JOB WILL RUN ON SINGLE CPU.
#
# *************************************************************
# *************************************************************
#
# Ex for PBS (job parameters start with a PBS directive):
#
# PBS -V
# PBS -l nodes=1:ppn=16,walltime=24:00:00
#
# Ex for SGE (job parameters start with $ sign):
#
# $ -N lncRNApipe
# $ -l num_threads=4
#
schedulerOpts:
# - $ -l mem_free=10G
 - $ -l num_threads=16

#clusterOpts:
# - module load lncRNApipe
#
# Specify if your reads are in FASTA or FASTQ format.
#
readType: FASTQ

#
# Specify if your reads are SE (single-end only), PE (paired-end only) or MIXED
#
libType: MIXED

#
# Specify if you want to use ENSEMBL or UCSC as source for annotation.
# "PLEASE MAKE SURE" that you are using the same sourceDB for tophat
# alignment, i.e. bowtie indexes created from the same sourceDB for the
# same assembly version. As downloding genome indices on-the-fly is time
# consuming and since many users may have genome indices installed for
# various NGS analysis anyways, we leave it to you to provide "CORRECT"
# genome index below in tophat and cufflinks options' configuration.
#
sourceDB: ENSEMBL

#
# Choose assembly version so that we can download up-to-date annotation on the fly.
# You can choose to supply your own annotation file for consistency below.
# ENSEMBL and UCSC represents species name differently in the URLs.
# To view species names for ENSEMBL do, "perl lncRNApipe --list ENSEMBL".
# Go to https://genome.ucsc.edu/FAQ/FAQreleases.html#TOP to view UCSC version names.
# For example, at UCSC, for mouse, it is mm9 or mm10, for rat, it is rn5 or rn6 etc...
#
species: Danio_rerio.Zv9.66

#
# If you want to use your own annoation file, provide full path to the annotation
# file of your choice. This option overrides "sourceDB: " and "species: " options above.
# Again, "PLEASE MAKE SURE", you are providing the same genome index from the
# same source. In the example below, "bowtieGenomeIndex" is rn4 genome index created
# from FASTA files from UCSC.
#
useThisAnnotation: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genes.gtf

#
# Provide Unix path to directory where the read files are located and also
# provide read file names.
# If your data is just SE, then disable "r2: " below by prefixing it with a #.
# Separate replicates of sample by a comma. Separate different samples by a |.
#
# PLEASE MAKE SURE THE READS ARE IN ORDER. DO NOT MIX AND MATCH READ ORDERS.
# WE HAVE NO WAY OF KNOWING WHICH READ FILE IS _1 or _2.
#
reads:
 readsDir: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/reads
 r1: 2cells_1_25000_reads.fq|6h_1_25000_reads.fq
 r2: 2cells_2_25000_reads.fq|6h_2_25000_reads.fq

#
# If you want to use TRIMMOMATIC to trim reads, then provide
# TRIMMOMATIC options. TRIMMOMATIC provides the following adapter
# files: NexteraPE-PE.fa, TruSeq2-PE.fa, TruSeq2-SE.fa, TruSeq3-PE-2.fa,
# TruSeq3-PE.fa and TruSeq3-SE.fa. Choose one below or provide full path
# to the adapter sequence file you want to use.
#
# No need to provide -threads, as it will be handled by lncRNApipe.
#
trimmomatic:
 - ILLUMINACLIP:TruSeq3-PE.fa:2:30:10
 - LEADING:20
 - TRAILING:20
 - SLIDINGWINDOW:5:20
 - MINLEN:25

#
# Provide bowtie genome index, full path to genome multi FASTA and tophat options.
# "PLEASE MAKE SURE" that you are using the same genome indices for the sourceDB
# mentioned above. Do not use UCSC genome indices if you requested ENSEMBL above in
# "sourceDB: " or vice versa.
#
# In the example below, it is assumed that you have already created a transcriptome
# index. If you have not created one, go through tophat manual on how to just create
# transcriptome index (https://ccb.jhu.edu/software/tophat/manual.shtml). If you
# use "--trancriptome-index" below and the index does not exist, it will keep overwriting
# while the jobs are running.
#
# No need to provide FASTQ files, as they will be handled by lncRNApipe.
# No need to provide -o, as it will be handled by lncRNApipe.
# No need to provide -p, as it will be handled by lncRNApipe.
#
genomeFasta: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genome.fa
bowtieGenomeIndex: /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/Danio_rerio.Zv9.66.dna
tophat:
 - --b2-sensitive
 - --transcriptome-index=/home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/Danio_rerio.Zv9.66
 - --no-coverage-search

#
# Provide cufflinks options and also "PLEASE MAKE SURE" you provide the same reference
# FASTA for the sourceDB you want to use in case of bias correction.
#
# No need to provide -g, as it will be handled by lncRNApipe.
# No need to provide -o, as it will be handled by lncRNApipe.
# No need to provide -p, as it will be handled by lncRNApipe.
# No need to provide input files, as they will be handled by lncRNApipe.
#
cufflinks:
 - -u
 - -b /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genome.fa
 - -g /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genes.gtf

#
# Provide cuffcompare options.
#
# ******************************** !! IMPORTANT !! ******************************
# *******************************************************************************
#
# If you only want to run lncRNApipe without the transcript assembly stage, then
# provide assembled transcripts in GTF format, otherwise, no options are needed.
#
# *******************************************************************************
# *******************************************************************************
#
# No need to provide -r, as it will be handled by lncRNApipe.
# Provide "-i transcript_assembly_list.txt" if you did not run assembly stage,
# where transcript_assembly_list.txt contains full path to assembled transcript
# files.
#
cuffcompare:
 - -i /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/assembly_list.txt

#
# Provide categorize_ncRNAs.pl options
# See "perl lncRNApipe -h cat" for description of options.
# 
categorize_ncRNAs:
 - -sample-names "2cells,6h"
 - -len 200
 - -min-exons 1
 - -ov 80
 - -inc
 - -ignore-genePred-err

#
# Provide get_unique_features.pl options.
# Generally only "-ov" is required in either
# case of [performTranscriptAssembly: YES] or
# [performTranscriptAssembly: NO].
#
# When you supply your own known ncRNAs file to
# compare against with "-sf", then you MUST also
# specify it's file format (Ex: gtf or bed) with
# "-sff" option.
# 
# See "perl lncRNApipe --h get" for description of options.
#
get_unique_features:
 - -ov 80
 - -sf /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/zf_noncode2016.gtf
 - -sff gtf

#
# By, default, RNAfold is not run since it is very slow.
# It is generally recommended to generate RNAfold plots
# based on the transcript of your interest after you have
# investigated the results, but you can still enable it
# in the pipeline by uncommenting "runRNAfold: YES" to
# run RNAfold with default options.
#
# To pass command line options to RNAfold, define it's
# after line "RNAfold:" 
#
# Mention any other option other than "-p" and "--noPS" as they
# are automatically handled by lncRNApipe.
#
# See "perl lncRNApipe -h rna" for description of options.
#
runRNAfold: YES
RNAfold:
# - --circ

#
# Provide options to cmscan. Running cmscan with
# default options provides good matches in
# most cases, but in any case you want to add
# extra options, do it here.
#
# To run cmscan with default options, use
# "runcmscan: YES".
#
# Add additional options you want to pass to cmscan
# after line "cmscan:". 
# Provide any options other than "-o", "--tblout"
# and "--cpu" as they are automatically handled by 
# lncRNApipe.
#
# See "perl lncRNApipe -h inf" for description of options.
#
runcmscan: YES
cmscan:
# - -E 9.0

#
# Provide cuffmerge options.
# If you have replicates, final predicted lncRNAs will be merged.
#
# No need to provide -s, as it will be handled by lncRNApipe.
# No need to provide -g, as it will be handled by lncRNApipe.
#
cuffmerge:
 - --min-isoform-fraction 0.05
 
#
# Provide cuffdiff options if you want to run differential expression
# tests between known ncRNAs and between novel ncRNAs in your samples.
# 
# Normally, cuffdiff is only run on identified known and novel ncRNAs.
# If you want to run cuffdiff on all transcripts, i.e to identify
# differentially expressed transcripts (end of typical tuxedo pipeline),
# then change "runCuffdiffForAllTranscripts" to YES. 
#
# If you have mentioned "-sample-names " above in "categorize_ncRNAs: ",
# no need to mention -L, else provide -L option here.
#
# No need to provide -o, as it will be handled by lncRNApipe.
# No need to provide -p, as it will be handled by lncRNApipe.
# No need to provide input files, if you have run tophat, cufflinks above.
#
# If "performTranscriptAssembly" is NO, then provide your own BAM files here prefixed by
# -bam option.
# Separate replicate BAM files with comma as you generally do with cuffdiff command.
#
runCuffdiffForAllTranscripts: YES
cuffdiff:
 - -u
 - -b /home/yeroslaviz/projects/MarcoN.RNASeq.GLD2/lncRNApipe//lncRNApipe-test/genome.fa

 Yes

# Looks like you failed 1 test of 1.
t/011_makemaker.t ..... 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests 

Test Summary Report
-------------------
t/010_module_build.t (Wstat: 256 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
t/011_makemaker.t   (Wstat: 256 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
Files=3, Tests=4,  1 wallclock secs ( 0.01 usr  0.00 sys +  0.57 cusr  0.06 csys =  0.64 CPU)
Result: FAIL
Failed 2/3 test programs. 2/4 subtests failed.
Makefile:873: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 1
-> FAIL Installing ExtUtils::CppGuess failed. See /home/bkimathi/.cpanm/work/1539265752.9094/build.log for details. Retry with --force to force install it.
-> FAIL Installing the dependencies failed: Module 'ExtUtils::CppGuess' is not installed
-> FAIL Bailing out the installation for Set-IntervalTree-0.12.
Expiring 4 work directories.


Set::IntervalTree                                                 ... FAIL