Error in cutadapt.py: "No such file or directory"

Here's the gist: https://gist.github.com/olgabot/b3589fa517407053461f
Here's just the error text:
ERROR 11:35:06,676 FunctionEdge - Error: cutadapt -f fastq --match-read-wildcards --times 2 '-e' '0'  '-O' '5'  '--quality-cutoff' '6'  '-m' '18'  '-b' 'TCGTATGCCGTCTTCTGCTTG' '-b' 'ATCTCGTATGCCGTCTTCTGCTTG' '-b' 'CGACAGGTTCAGAGTTCTACAGTCCGACGATC' '-b' 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' '-b' 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA' '-b' 'TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT'  '-o' '/home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_se_v1/CVN_01.polyATrim.adapterTrim.fastq'  '/home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_se_v1/CVN_01'  > CVN_01.polyATrim.adapterTrim.metrics 
ERROR 11:35:06,790 FunctionEdge - Contents of /home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_se_v1/CVN_01.polyATrim.adapterTrim.fastq.out:
discarding /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/olga/bin to PATH
discarding /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/olga/bin to PATH
Traceback (most recent call last):
  File "/projects/ps-yeolab/software/bin/cutadapt", line 10, in <module>
    cutadapt.main()
  File "/home/yeo-lab/software/lib/python2.7/site-packages/cutadapt/scripts/cutadapt.py", line 769, in main
    reader = read_sequences(input_filename, quality_filename, colorspace=options.colorspace, fileformat=options.format)
  File "/home/yeo-lab/software/lib/python2.7/site-packages/cutadapt/scripts/cutadapt.py", line 247, in read_sequences
    return seqio.SequenceReader(seqfilename, colorspace, fileformat)
  File "/home/yeo-lab/software/lib/python2.7/site-packages/cutadapt/seqio.py", line 161, in SequenceReader
    return fastq_reader(file)
  File "/home/yeo-lab/software/lib/python2.7/site-packages/cutadapt/seqio.py", line 295, in __init__
    file = xopen(file, "r")
  File "/home/yeo-lab/software/lib/python2.7/site-packages/cutadapt/xopen.py", line 47, in xopen
    return open(filename, mode)
IOError: [Errno 2] No such file or directory: '/home/obotvinnik/projects/singlecell_pnms/analysis/singlecell_pnms_se_v1/CVN_01'
Nodes:        tscc-1-33
discarding /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/bin from PATH
prepending /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/olga/bin to PATH 
ERROR 11:35:06,808 QGraph - Uncaught error running jobs. 
java.lang.NoClassDefFoundError: org/broadinstitute/sting/queue/engine/QGraph$$anonfun$runJobs$3$$anonfun$apply$4
        at org.broadinstitute.sting.queue.engine.QGraph$$anonfun$runJobs$3.apply(QGraph.scala:479)
        at org.broadinstitute.sting.queue.engine.QGraph$$anonfun$runJobs$3.apply(QGraph.scala:472)
        at scala.collection.immutable.HashSet$HashSet1.foreach(HashSet.scala:130)
        at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:275)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:472)
        at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:156)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scala:171)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
        at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)
Have you run into this before? Does this mean you need to create a folder for each sample?
YeoLab / gscripts

Error in cutadapt.py: "No such file or directory" #53
