Here is an example of error message I got from doing adaptor trimming:
STARTING cutadapt_raw_files
cutadapt -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o /restricted/projectnb/montilab-p/personal/liye/others/bifurcat
ion-MDAMB231/results/cutadapt/SRR1481939.clipped.fastq.gz -p /restricted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/results/cutadapt/SRR1481939.clipped.2.fastq.gz /restr
icted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/SRR1481939_1.fastq /restricted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/SRR1481939_2.fastqTracebac
k (most recent call last):
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/bin/cutadapt", line 11, in
load_entry_point('cutadapt==1.12', 'console_scripts', 'cutadapt')()
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 568, in load_entry_point
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2720, in load_entry_point
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2380, in load
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2386, in resolve
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/scripts/cutadapt.py", line 62,
in
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/init.py", line 11, in chec
k_importability
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/_align.py", line 7, in <module
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/_align.py", line 4, in boots
trap
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1171, in resource_filename
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1879, in get_resource_filename
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1909, in _extract_resource
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1237, in get_cache_path
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 1217, in extraction_error
pkg_resources.ExtractionError: Can't extract file(s) to egg cache
The following error occurred while trying to extract file(s) to the Python egg
cache:
The Python egg cache directory is currently set to:
/usr2/postdoc/zhangliy/.python-eggs
Perhaps your account does not have write access to this directory? You can
change the cache directory by setting the PYTHON_EGG_CACHE environment
variable to point to an accessible directory.
ERROR: Could not find the output file
I skip the adaptor trimming to test the following steps.
Here is an example of error message I got from doing adaptor trimming: STARTING cutadapt_raw_files cutadapt -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o /restricted/projectnb/montilab-p/personal/liye/others/bifurcat ion-MDAMB231/results/cutadapt/SRR1481939.clipped.fastq.gz -p /restricted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/results/cutadapt/SRR1481939.clipped.2.fastq.gz /restr icted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/SRR1481939_1.fastq /restricted/projectnb/montilab-p/personal/liye/others/bifurcation-MDAMB231/SRR1481939_2.fastqTracebac k (most recent call last): File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/bin/cutadapt", line 11, in
load_entry_point('cutadapt==1.12', 'console_scripts', 'cutadapt')()
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 568, in load_entry_point
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2720, in load_entry_point
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2380, in load
File "build/bdist.linux-x86_64/egg/pkg_resources/init.py", line 2386, in resolve
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/scripts/cutadapt.py", line 62,
in
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/init.py", line 11, in chec
k_importability
File "/restricted/projectnb/montilab-p/personal/liye/shared/pipeline/hydra/dev_env/lib/python2.7/site-packages/cutadapt-1.12-py2.7-linux-x86_64.egg/cutadapt/_align.py", line 7, in <module
The following error occurred while trying to extract file(s) to the Python egg cache:
[Errno 17] File exists: '/usr2/postdoc/zhangliy/.python-eggs/cutadapt-1.12-py2.7-linux-x86_64.egg-tmp'
The Python egg cache directory is currently set to:
/usr2/postdoc/zhangliy/.python-eggs
Perhaps your account does not have write access to this directory? You can change the cache directory by setting the PYTHON_EGG_CACHE environment variable to point to an accessible directory.
ERROR: Could not find the output file
I skip the adaptor trimming to test the following steps.