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
  [Errno 2] No such file or directory: 'HP_SAMPLES1.sam'
  [Exception type: FileNotFoundError, raised in count.py:58]
  [Errno 2] No such file or directory: 'HP_SAMPLES2.sam'
  [Exception type: FileNotFoundError, raised in count.py:58]
  [Errno 2] No such file or directory: 'HPSM_SAMPLES1.sam'
  [Exception type: FileNotFoundError, raised in count.py:58]
  [Errno 2] No such file or directory: 'HPSM_SAMPLES2.sam'
  [Exception type: FileNotFoundError, raised in count.py:58]
mkdir: cannot create directory ‘alignment’: File exists
mv: cannot stat ‘*.sam’: No such file or directory
mkdir: cannot create directory ‘figures’: File exists
mkdir: cannot create directory ‘kegg_analysis’: File exists
mkdir: cannot create directory ‘rnaseq_analysis’: File exists
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
