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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Error and no QC following 3 replicate PE run #62

Closed rbronste closed 7 years ago

rbronste commented 7 years ago

Hi Jin,

Quick question, ran the pipeline in the following way and got the following error after each replicate stage (3 PE replicates) finished, and wound up with no QC or Macs peaks but most of the other output as far as I can tell:

bds atac.bds -species mm10 -nth 16 -mapq_thresh 20 -no_dup_removal -chrsz /sonas-hs/tollkuhn/hpc_norepl/home/rbronste/mm10.chrom.sizes -gensz mm

Gpr.reader(565):    File not found '/mnt/grid/tollkuhn/hpc_norepl/home/data/rbronste/atac_dnase_pipelines/out/qc/rep1/298765_S1_R1_001_dedup.trim.PE2SE.nodup.pbc.qc'
Fatal error: modules/log_parser.bds, line 244, pos 34. Trying to access element number 0 from list 'arr' (list size: 0).

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
Fatal error: modules/ENCODE_accession.bds, line 184, pos 25. Map 'map_pbc' does not have key 'PBC1'.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.
Fatal error: atac.bds, line 385, pos 2. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done.

Thanks!

Rob.

rbronste commented 7 years ago

I just noticed I did not have the bool of 1 for -no_dup_removal, could that have been the cause?

leepc12 commented 7 years ago

No, -no_dup_removal 1 should work correctly, but it's a flag so I recommend not to add 1.

I think I fixed it in the commit 1bef188. Please try with the latest pipeline.

rbronste commented 7 years ago

You fixed the reason for that error above?

leepc12 commented 7 years ago

Yes, I pushed that commit an hour ago..