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benedictpaten / marginAlign

UCSC Nanopore
MIT License
42 stars 13 forks source link

Error: sees to be looking for enriron.pickle at the wrong location #38

Closed cliu32 closed 6 years ago

cliu32 commented 6 years ago

Hi, I was trying to run the basic command line: marginAlign fastqfile fastaRef test.sam --jobTree ./jobTree but ran into the following error message and the program stalled. Process Process-1: Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, self._kwargs) File "/home/username/exp/marginAlign/submodules/jobTree/batchSystems/singleMachine.py", line 51, in worker slaveMain() File "/home/username/exp/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 103, in main fileHandle = open(getEnvironmentFileName(jobTreePath), 'r') IOError: [Errno 2] No such file or directory: '/media/username/Seagate/environ.pickle'** I could not understand the error message becuase I was running the program at this location '/media/username/Seagate Backup Plus Drive/ONTreads/experiment1207/testmargin/' and I can see the jobTree folder created there. But the program seems to be looking for environ.pickle at '/media/username/Seagate/'. How can I fix this problem? Thank you so much for your help!

mitenjain commented 6 years ago

Hello,

Are you using a virtualenv? If not, could you try using it?

If you could send me some test data I can try and reproduce the error on our end. This will help us debug the issue.

Thank you.

cliu32 commented 6 years ago

Thanks for the quick response. I moved the job from my external hard drive to the internal hard drive, and the problem disappeared. But I got the following error message: log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: lastdb: bad symbol: - I do have '-' in my fasta reference file as spacerholders between two exons. Is there a way to keep these placeholders? Thanks and happy new year.

mitenjain commented 6 years ago

There isn't at the moment I am afraid. You could substitute that with an N and bwa will align it (I think minimap2 will as well). Not sure how that plays with downstream processing since marginAlign presently isn't compatible with the splice-aware CIGAR strings.