Comments (5)
From [email protected] on March 27, 2012 05:35:58
If you run cutadapt by giving its absolute or relative path (./cutadapt in your case) on the command line, then installation is not required (the installed version is not even used in this case).
The SyntaxError is a bit strange. I think it occurs when a Python 3 program is run under Python 2. Please try to specify the Python interpreter explicitly by running cutadapt like this:
python2.6 cutadapt
What does the command
python -V
say?
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From [email protected] on April 02, 2012 23:28:41
Hi, any news on this? I'm willing to fix this, but since I've never encountered the problem, I'd need your help.
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From [email protected] on April 17, 2012 00:53:21
Status: Invalid
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From [email protected] on April 17, 2012 08:08:59
I was getting the exact same error until I realized it was a python version issue since our default python installation is v2.4.3. I followed your instructions, using v2.6.4:
/apps/python-2.6.4/bin/python2.6 setup.py build_ext -i
Then I called ./cutadapt and got the error above. Of course the correct command is:
/apps/python-2.6.4/bin/python2.6 ./cutadapt --help
Seems to work fine...
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From [email protected] on April 18, 2012 09:40:31
Thanks, I have updated the FAQ and the README to help others who have the same problem.
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Related Issues (20)
- Remove the "Incomplete adapter sequence" warning
- Nanopore adapter detection HOT 1
- "OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads HOT 7
- Unexpected trimming behavior HOT 5
- cutadapt: error: cutadapt not able to trim the desired adapto HOT 3
- Error in FASTQ file at line 20136: Length of sequence and qualities differ HOT 2
- Adapter matches in the middle of a read masked with N HOT 2
- Feature request: shorten paired-end reads with separate values for --length HOT 1
- Help to get accurate counts of demultiplexed amplicons using cutadapt HOT 2
- Adapters in form of file and linked mode HOT 4
- Problems reading stdin on Windows 11 Python 3.12 HOT 5
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- Using --revcomb on paired-end data HOT 1
- Issue importing fasta files to Cutadapt virtual environment HOT 1
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- Should I use -a or -g when demultiplexing ONT reads with dual barcodes? HOT 3
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