Gina Pham

I ran this in debug mode a few times and got this type of error message in the Jelly.py error log: 2019-03-18 13:24:31,945 [DEBUG] CommandRunner Returned: [(137, '/bin/sh: line 1: 38454 Killed Extraction.py /data/scratch/gpham/pepsi_dm/pbjelly/jelly_protocol3.xml --debug > /data/scratch/gpham/pepsi_dm/pbjelly/dm5_unmasked_hic_oriented_gapfill/assembly/extraction.out 2> /data/scratch/gpham/pepsi_dm/pbjelly/dm5_unmasked_hic_oriented_gapfill/assembly/extraction.err\n', None)] It looked like a memory...

I cannot get the "extraction" step to finish. The log in assembly/extraction.err shows this as the last line: 2019-03-15 16:11:57,053 [INFO] Parsing /data/scratch/gpham/pepsi_dm/pbjelly/all_dm_pacbio_concat_ec2.fasta There are no messages following this line. Any ideas as to what could be wrong?