ryanabo
commented
9 years ago I am sorry for your troubles with the software! Thank you for reporting this bug. It is now fixed in the master branch. Please pull this down again and test. Let me know if there are any other issues.
Hi I would like to run Breakmer and validate some results. I am just sticking since I get in the very beginning this error. Cutadapt and Jellifish are running and in my PATH.
Thanks for your help Alessandro
python ~/bin/breakmer/breakmer.py run -c breakmer.cfg Traceback (most recent call last): File "/cbio/cslab/home/pastore/bin/breakmer/breakmer.py", line 70, in
RUN_TRACKER = breakmer_analysis.RunTracker(params.ParamManager(PARSER.parse_args()))
File "/cbio/cslab/home/pastore/bin/breakmer/breakmer/params.py", line 51, in init
self.set_params(arguments)
File "/cbio/cslab/home/pastore/bin/breakmer/breakmer/params.py", line 103, in set_params
self.check_binaries() # Check if Jellyfish and Cutadapt work.
File "/cbio/cslab/home/pastore/bin/breakmer/breakmer/params.py", line 201, in check_binaries
self.set_param(binary, binaryCheck) # Store the result in the opts dictionary.
NameError: global name 'binary' is not defined
-bash-4.1$ jellyfish --version jellyfish 2.2.3 -bash-4.1$ jellyfish --help Usage: jellyfish [options] arg...
Where is one of: count, bc, info, stats, histo, dump, merge, query, cite, mem, jf.
Options:
--version Display version
--help Display this message
-bash-4.1$ cutadapt cutadapt version 1.8.3 Copyright (C) 2010-2015 Marcel Martin marcel.martin@scilifelab.se
cutadapt removes adapter sequences from high-throughput sequencing reads.
Usage: cutadapt -a ADAPTER [options] [-o output.fastq] input.fastq
For paired-end reads: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq
Replace "ADAPTER" with the actual sequence of your 3' adapter. IUPAC wildcard characters are supported. The reverse complement is not automatically searched. All reads from input.fastq will be written to output.fastq with the adapter sequence removed. Adapter matching is error-tolerant. Multiple adapter sequences can be given (use further -a options), but only the best-matching adapter will be removed.
Input may also be in FASTA format. Compressed input and output is supported and auto-detected from the file name (.gz, .xz, .bz2). Use the file name '-' for standard input/output. Without the -o option, output is sent to standard output.
Some other available features are:
Use "cutadapt --help" to see all command-line options. See http://cutadapt.readthedocs.org/ for full documentation.