Run Errors

[iminkin]

I tried to run progressiveCactus on Ubuntu 12.04.3 LTS, 64 bit, Python 2.7.3 just installed from scratch. I tried to run it on two small bacterial genomes, Helicobacter Pylori F32 and Helicobacter Pylori Gambia.

I ran:

./bin/runProgressiveCactus.sh ./work/seqfile2 ./temp ./out.hal

And got following output:

Beginning Alignment Beginning HAL Export There are 2 active jobs, 1 parent jobs with children, 2 totally failed jobs and 0 empty jobs (i.e. finished but not cleaned up) currently in job tree: ./temp/jobTree Error: Command: . ./bin/../src/../environment && cactus2hal.py ./temp/progressiveAlignment/progressiveAlignment_project.xml ./out.hal >> ./temp/cactus.log 2>&1 exited with non-zero status 1

Temporary data was left in: ./temp More information can be found in ./temp/cactus.log

Directory "temp": https://docs.google.com/file/d/0BwczEe34tHjOVDBfaFJ4MlJEWUU/edit?usp=sharing

Directory "work": https://docs.google.com/file/d/0BwczEe34tHjOa0pVWW1qdXhCT3M/edit?usp=sharing

[glennhickey]

Hi Ilya,

The problem seems to be that your input FASTA files end with both carriage returns and newline characters (probably due being written in Windows), whereas our Linux software is expecting only the latter. This is leads to an assertion error, cryptically buried in cactus.log.

Thanks for pointing this out. We will need to 1) clean up this error message and 2) add support to explicitly ignore the carriage returns. If you want to run on these sequences in the meantime, you can do that by stripping out all the carriage returns.

-Glenn

On Thu, Oct 17, 2013 at 3:38 AM, Ilya Minkin notifications@github.comwrote:

I tried to run progressiveCactus on 12.04.3 LTS, 64 bit, Python 2.7.3 just installed from scratch. I tried to run it on two small bacterial genomes, Helicobacter Pylori F32 and Helicobacter Pylori Gambia.

I ran:

./bin/runProgressiveCactus.sh ./work/seqfile2 ./temp ./out.hal

And got following output:

Beginning Alignment Beginning HAL Export There are 2 active jobs, 1 parent jobs with children, 2 totally failed jobs and 0 empty jobs (i.e. finished but not cleaned up) currently in job tree: ./temp/jobTree Error: Command: . ./bin/../src/../environment && cactus2hal.py ./temp/progressiveAlignment/progressiveAlignment_project.xml ./out.hal >> ./temp/cactus.log 2>&1 exited with non-zero status 1

Temporary data was left in: ./temp More information can be found in ./temp/cactus.log

Directory "temp": https://docs.google.com/file/d/0BwczEe34tHjOVDBfaFJ4MlJEWUU/edit?usp=sharing

Directory "work": https://docs.google.com/file/d/0BwczEe34tHjOa0pVWW1qdXhCT3M/edit?usp=sharing

— Reply to this email directly or view it on GitHubhttps://github.com/glennhickey/progressiveCactus/issues/5 .

[joelarmstrong]

Oops -- I am a bit hopeless with github--but the carriage returns are the problem.

To easily strip them out, run:

sudo apt-get install dos2unix
dos2unix work/Gambia.fasta
dos2unix work/F32.fasta

[iminkin]

Thank you for the help, changing format of line endings worked.