doit database deadlock

[johnsolk]

khmer_env)ljcohen@c8-22:~/dammit$ dammit annotate A_xenica.Trinity.fixed.fa --user-databases protein.fa --busco-group metazoa --n_threads 4

dammit! a tool for easy de novo transcriptome annotation Camille Scott 2015

submodule: annotate

--- Checking PATH for dependencies

      [x] HMMER

      [x] Infernal

      [x] BLAST+

      [x] BUSCO

      [x] TransDecoder

      [x] LAST

      [x] crb-blast

--- Dependency results

      All dependencies satisfied!

--- Checking for database prep (dir: /home/ljcohen/.dammit/databases)

      [x] download_and_gunzip:Pfam-A.hmm

      [x] hmmpress:Pfam-A.hmm

      [x] download_and_gunzip:Rfam.cm

      [x] cmpress:Rfam.cm

      [x] download_and_gunzip:aa_seq_euk.fasta

      [x] lastdb:aa_seq_euk.fasta.db

      [x] download_and_gunzip:ODB8_EukOGs_genes_ALL_levels.txt

      [x] download_and_untar:databases-metazoa

--- Database results

      All databases prepared!

--- Running annotate!

      Transcriptome file: A_xenica.Trinity.fixed.fa

      Output directory: /home/ljcohen/dammit/A_xenica.Trinity.fixed.fa.dammit

      [x] A_xenica.Trinity.fixed.fa

      [x] transcriptome_stats:A_xenica.Trinity.fixed.fa

      [x] busco:A_xenica.Trinity.fixed.fa-metazoa

      [ ] TransDecoder.LongOrfs:A_xenica.Trinity.fixed.fa

      [ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^C^CException KeyboardInterrupt in <bound method Popen.del of <subprocess.Popen object at 0x2ac92865dc50>> ignored Traceback (most recent call last): File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/doit_cmd.py", line 168, in run return command.parse_execute(args) File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/cmd_base.py", line 122, in parse_execute return self.execute(params, args) File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/cmd_base.py", line 405, in execute return self._execute(**exec_params) File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/cmd_run.py", line 253, in _execute return runner.run_all(self.control.task_dispatcher()) File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/runner.py", line 252, in run_all self.finish() File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/runner.py", line 232, in finish self.dep_manager.close() File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/dependency.py", line 509, in close self.backend.dump() File "/home/ljcohen/anaconda2/envs/khmer_env/lib/python2.7/site-packages/doit/dependency.py", line 340, in dump (task_id, json.dumps(self._cache[task_id]))) OperationalError: database is locked ^C

[camillescott]

Still not sure how to fix this or what triggers it; just gonna leave it here now until it can be reproduced.