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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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bplapply error in runSCENIC_2_createRegulons #47

Closed SamAllon closed 5 years ago

SamAllon commented 5 years ago

The early steps of Scenic appear to have worked well on my dataset of ~350 cells, using a server session with access to 50GB RAM. However, the following error appeared >12 hours into running the runSCENIC_2_createRegulons function:

> runSCENIC_2_createRegulons(scenicOptions)
08:44   Step 2. Identifying regulons
tfModulesSummary:

 top5perTarget          top50 top10perTarget           w005 top50perTarget
           417            443            835            959            963
          w001
           963
08:45   RcisTarget: Calculating AUC
Scoring database:  [Source file: mm9-500bp-upstream-7species.mc9nr.feather]
Scoring database:  [Source file: mm9-tss-centered-10kb-7species.mc9nr.feather]
22:46   RcisTarget: Adding motif annotation
Error: 'bplapply' receive data failed:
  error reading from connection

Has anyone encountered this before?

SamAllon commented 5 years ago

Solution (prior to the runSCENIC_2_createRegulons command): BiocParallel::register(BiocParallel::SerialParam())