2017-04-13 09:20:07,908 [INFO] Running /gscratch/srlab/programs/PBSuite/bin/Jelly.py mapping /gscratch/srlab/data/Oly_gap_filling/Protocol.xml

Please Cite: English, Adam C., Stephen Richards, Yi Han, Min Wang,
             Vanesa Vee, Jiaxin Qu, Xiang Qin, et al. "Mind the
             Gap: Upgrading Genomes with Pacific Biosciences RS
             Long-Read Sequencing Technology." PLoS ONE 7, no. 11
             (November 21, 2012): e47768.
             doi:10.1371/journal.pone.0047768.

[WARNING] Couldn't find /gscratch/srlab/data/Oly_gap_filling/scaffold.qual... assuming there isn't a quality file for the reference
2017-04-13 09:20:07,920 [INFO] Executing Stage: mapping
2017-04-13 09:20:07,922 [INFO] Running blasr
2017-04-13 09:20:07,922 [CRITICAL] Specified reference.sa /gscratch/srlab/data/Oly_gap_filling/scaffold.fasta.sa does not exists. Mapping will be slower
2017-04-13 09:20:07,935 [WARNING] Output File /gscratch/srlab/data/Oly_gap_filling/output/mapping/170210_PCB-CC_MS_EEE_20kb_P6v2_D01_1_filtered_subreads.fastq.m4 already exists and will be overwritten.
slurmstepd: error: *** JOB 7307 ON n2076 CANCELLED AT 2017-04-13T09:20:26 ***