GCC/7.3.0-2.30(23):ERROR:150: Module 'GCC/7.3.0-2.30' conflicts with the currently loaded module(s) 'GCC/8.3.0'
GCC/7.3.0-2.30(23):ERROR:102: Tcl command execution failed: conflict GCC

GCC/7.3.0-2.30(23):ERROR:150: Module 'GCC/7.3.0-2.30' conflicts with the currently loaded module(s) 'GCC/8.3.0'
GCC/7.3.0-2.30(23):ERROR:102: Tcl command execution failed: conflict GCC

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCC/7.3.0-2.30(23):ERROR:150: Module 'GCC/7.3.0-2.30' conflicts with the currently loaded module(s) 'GCC/8.3.0'
GCC/7.3.0-2.30(23):ERROR:102: Tcl command execution failed: conflict GCC

GCC/7.3.0-2.30(23):ERROR:150: Module 'GCC/7.3.0-2.30' conflicts with the currently loaded module(s) 'GCC/8.3.0'
GCC/7.3.0-2.30(23):ERROR:102: Tcl command execution failed: conflict GCC

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

GCCcore/7.3.0(23):ERROR:150: Module 'GCCcore/7.3.0' conflicts with the currently loaded module(s) 'GCCcore/8.3.0'
GCCcore/7.3.0(23):ERROR:102: Tcl command execution failed: conflict GCCcore

foss/2019b(24):ERROR:150: Module 'foss/2019b' conflicts with the currently loaded module(s) 'foss/2018b'
foss/2019b(24):ERROR:102: Tcl command execution failed: conflict foss

foss/2019b(24):ERROR:150: Module 'foss/2019b' conflicts with the currently loaded module(s) 'foss/2018b'
foss/2019b(24):ERROR:102: Tcl command execution failed: conflict foss

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

expat/2.2.7-GCCcore-8.3.0(28):ERROR:150: Module 'expat/2.2.7-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'expat/2.2.5-GCCcore-7.3.0'
expat/2.2.7-GCCcore-8.3.0(28):ERROR:102: Tcl command execution failed: conflict expat

libffi/3.2.1-GCCcore-8.3.0(28):ERROR:150: Module 'libffi/3.2.1-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'libffi/3.2.1-GCCcore-7.3.0'
libffi/3.2.1-GCCcore-8.3.0(28):ERROR:102: Tcl command execution failed: conflict libffi

util-linux/2.34-GCCcore-8.3.0(22):ERROR:150: Module 'util-linux/2.34-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'util-linux/2.32-GCCcore-7.3.0'
util-linux/2.34-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict util-linux

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

FFTW/3.3.8-gompi-2019b(24):ERROR:150: Module 'FFTW/3.3.8-gompi-2019b' conflicts with the currently loaded module(s) 'FFTW/3.3.8-gompi-2018b'
FFTW/3.3.8-gompi-2019b(24):ERROR:102: Tcl command execution failed: conflict FFTW

gompi/2019b(24):ERROR:150: Module 'gompi/2019b' conflicts with the currently loaded module(s) 'gompi/2018b'
gompi/2019b(24):ERROR:102: Tcl command execution failed: conflict gompi

expat/2.2.7-GCCcore-8.3.0(28):ERROR:150: Module 'expat/2.2.7-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'expat/2.2.5-GCCcore-7.3.0'
expat/2.2.7-GCCcore-8.3.0(28):ERROR:102: Tcl command execution failed: conflict expat

X11/20190717-GCCcore-8.3.0(22):ERROR:150: Module 'X11/20190717-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'X11/20180604-GCCcore-7.3.0'
X11/20190717-GCCcore-8.3.0(22):ERROR:102: Tcl command execution failed: conflict X11

expat/2.2.7-GCCcore-8.3.0(28):ERROR:150: Module 'expat/2.2.7-GCCcore-8.3.0' conflicts with the currently loaded module(s) 'expat/2.2.5-GCCcore-7.3.0'
expat/2.2.7-GCCcore-8.3.0(28):ERROR:102: Tcl command execution failed: conflict expat

foss/2019b(24):ERROR:150: Module 'foss/2019b' conflicts with the currently loaded module(s) 'foss/2018b'
foss/2019b(24):ERROR:102: Tcl command execution failed: conflict foss

gompi/2019b(24):ERROR:150: Module 'gompi/2019b' conflicts with the currently loaded module(s) 'gompi/2018b'
gompi/2019b(24):ERROR:102: Tcl command execution failed: conflict gompi

stat: Bad file descriptor
Warning: Could not open read file "/data/mramseylab/RNAseq/transcriptome_analyses/hp_sm_aerobicHP1_R1.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
stat: Bad file descriptor
Warning: Could not open read file "/data/mramseylab/RNAseq/transcriptome_analyses/hp_sm_aerobicHP2_R1.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
stat: Bad file descriptor
Warning: Could not open read file "/data/mramseylab/RNAseq/transcriptome_analyses/hp_sm_aerobicHPSM1_R1.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
stat: Bad file descriptor
Warning: Could not open read file "/data/mramseylab/RNAseq/transcriptome_analyses/hp_sm_aerobicHPSM2_R1.fastq" for reading; skipping...
Error: No input read files were valid
(ERR): bowtie2-align exited with value 1
Traceback (most recent call last):
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/bin/htseq-count", line 3, in <module>
    import HTSeq.scripts.count
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/HTSeq/__init__.py", line 13, in <module>
    from HTSeq._HTSeq import *
  File "__init__.pxd", line 164, in init HTSeq._HTSeq
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: libgfortran.so.4: cannot open shared object file: No such file or directory

Traceback (most recent call last):
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/bin/htseq-count", line 3, in <module>
    import HTSeq.scripts.count
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/HTSeq/__init__.py", line 13, in <module>
    from HTSeq._HTSeq import *
  File "__init__.pxd", line 164, in init HTSeq._HTSeq
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: libgfortran.so.4: cannot open shared object file: No such file or directory

Traceback (most recent call last):
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/bin/htseq-count", line 3, in <module>
    import HTSeq.scripts.count
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/HTSeq/__init__.py", line 13, in <module>
    from HTSeq._HTSeq import *
  File "__init__.pxd", line 164, in init HTSeq._HTSeq
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: libgfortran.so.4: cannot open shared object file: No such file or directory

Traceback (most recent call last):
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 16, in <module>
    from . import multiarray
ImportError: libgfortran.so.4: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/bin/htseq-count", line 3, in <module>
    import HTSeq.scripts.count
  File "/opt/software/HTSeq/0.11.2-foss-2018b-Python-3.6.6/lib/python3.6/site-packages/HTSeq/__init__.py", line 13, in <module>
    from HTSeq._HTSeq import *
  File "__init__.pxd", line 164, in init HTSeq._HTSeq
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/__init__.py", line 142, in <module>
    from . import add_newdocs
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/__init__.py", line 8, in <module>
    from .type_check import *
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/lib/type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "/opt/software/Python/3.6.6-foss-2018b/lib/python3.6/site-packages/numpy-1.15.0-py3.6-linux-x86_64.egg/numpy/core/__init__.py", line 26, in <module>
    raise ImportError(msg)
ImportError: 
Importing the multiarray numpy extension module failed.  Most
likely you are trying to import a failed build of numpy.
If you're working with a numpy git repo, try `git clean -xdf` (removes all
files not under version control).  Otherwise reinstall numpy.

Original error was: libgfortran.so.4: cannot open shared object file: No such file or directory

mv: cannot stat ‘*.sam’: No such file or directory
Loading required package: S4Vectors
Loading required package: stats4
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, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Error in read.table(file.path(directory, fn), fill = TRUE) : 
  no lines available in input
Calls: DESeqDataSetFromHTSeqCount -> lapply -> lapply -> FUN -> read.table
Execution halted
