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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
51 stars 13 forks source link

lock file Problem #238

Open AnthonyPhosphate opened 1 year ago

AnthonyPhosphate commented 1 year ago

PEPATAC_log.txt I have used pepatac many times before to process ATAC data, and this time I am running this pipeline but encountering same error over and over again: file lock during prealignment step 

> Found lock file: /home/dongyucheng/data/ATAC/0316_hepG2/result/results_pipeline/Met200_24h-1/lock.prealignments__Met200_24h-1_rCRSd_bt_aln_summary.log
> Waiting for file lock: /home/dongyucheng/data/ATAC/0316_hepG2/result/results_pipeline/Met200_24h-1/lock.prealignments__Met200_24h-1_rCRSd_bt_aln_summary.log (03-26 11:08:35) elapsed: 0.0 _TIME_
> This indicates that another process may be executing this command, or the pipeline was not properly shut down.  If the pipeline was not properly shut down last time, you should restart it in 'recover' mode (-R) to indicate that this step should be restarted.

. I am running pepatac for the first time in the target output path, and the previous run was not interrupted. Flag in the results_pipeline shows PEPATAC_waiting.flag. Thanks for developing such a good package, hope you can help me out!

AnthonyPhosphate commented 1 year ago

seams the pipeline is stuck at this step perl /home/dongyucheng/tools/pepatac/tools/filter_paired_fq.pl htop shows a running process with zero CPU or Mem occupation.