AttributeError: 'Expando' object has no attribute 'bamqc'

[hmkim]

Hello!

When I turn on the save-bam option, I got the error in below.

save-bam: true

WARNING:toil.leader:9/H/jobIJzf6M Traceback (most recent call last): WARNING:toil.leader:9/H/jobIJzf6M File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/worker.py", line 314, in workerScript WARNING:toil.leader:9/H/jobIJzf6M job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) WARNING:toil.leader:9/H/jobIJzf6M File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/job.py", line 1351, in _runner WARNING:toil.leader:9/H/jobIJzf6M returnValues = self._run(jobGraph, fileStore) WARNING:toil.leader:9/H/jobIJzf6M File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/job.py", line 1296, in _run WARNING:toil.leader:9/H/jobIJzf6M return self.run(fileStore) WARNING:toil.leader:9/H/jobIJzf6M File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/job.py", line 1480, in run WARNING:toil.leader:9/H/jobIJzf6M rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs) WARNING:toil.leader:9/H/jobIJzf6M File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil_rnaseq/toil_rnaseq.py", line 111, in workflow WARNING:toil.leader:9/H/jobIJzf6M save_bam = any([config.save_bam, config.bamqc]) WARNING:toil.leader:9/H/jobIJzf6M AttributeError: 'Expando' object has no attribute 'bamqc' WARNING:toil.leader:9/H/jobIJzf6M ERROR:toil.worker:Exiting the worker because of a failed job on host soybean WARNING:toil.leader:9/H/jobIJzf6M WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'workflow' 9/H/jobIJzf6M with ID 9/H/jobIJzf6M to 0 WARNING:toil.leader:Job 'workflow' 9/H/jobIJzf6M with ID 9/H/jobIJzf6M is completely failed INFO:toil.leader:Finished toil run with 3 failed jobs. INFO:toil.leader:Failed jobs at end of the run: 'workflow' 9/H/jobIJzf6M 'workflow' s/L/jobgsFPOB 'map_job' c/Q/jobxHWc99 Traceback (most recent call last): File "/BiO/BioPeople/brandon/venv_toil/bin/toil-rnaseq", line 11, in sys.exit(main()) File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil_rnaseq/toil_rnaseq.py", line 214, in main toil.start(Job.wrapJobFn(map_job, workflow, samples, config)) File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/common.py", line 784, in start return self._runMainLoop(rootJobGraph) File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/common.py", line 1059, in _runMainLoop jobCache=self._jobCache).run() File "/BiO/BioPeople/brandon/venv_toil/local/lib/python2.7/site-packages/toil/leader.py", line 237, in run raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) toil.leader.FailedJobsException

Could you check this issue ?

[jvivian]

Hi @hmkim — Is there a chance you're using an older config file with a newer version of the workflow? The newest version of the workflow has a bamqc option in the config that was reintroduced in version 4.1. Below the fastqc option you should see:

# If true, will run UMEND BamQC and include statistics about Uniquely Mapped Exonic Non-Duplicate (UMEND) reads
# If bamqc and save-bam are enabled, a bam with duplicates marked (output of BAMQC) is saved
bamqc: 

If that's not the case, please let me know so I can do some internal testing.

[hmkim]

@jvivian Thank you. I solved this issue by your suggestion.