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roblanf / minion_qc

Quality control for MinION sequencing data
MIT License
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Can't successfully run the examples #39

Closed LinXialab closed 4 years ago

LinXialab commented 6 years ago

Hi, I'm try to run the script just on example data as followed: Rscript MinIONQC.R -i example_input -o ./ -p 2 (The version of my R is 3.4.3)

But it is not successful, and i got some error information as followed:

INFO [2018-09-29 15:54:39] Analysing the following files INFO [2018-09-29 15:54:39] /home/xialin/tools/minion_qc-master/example_input//RB7_A2/sequencing_summary.txt INFO [2018-09-29 15:54:39] /home/xialin/tools/minion_qc-master/example_input//RB7_D3/sequencing_summary.txt INFO [2018-09-29 15:54:39] Loading input file: /home/xialin/tools/minion_qc-master/example_input//RB7_A2/sequencing_summary.txt INFO [2018-09-29 15:54:39] Loading input file: /home/xialin/tools/minion_qc-master/example_input//RB7_D3/sequencing_summary.txt INFO [2018-09-29 15:54:46] RB7_A2: creating output directory:.//RB7_A2 INFO [2018-09-29 15:54:46] RB7_A2: summarising input file for flowcell INFO [2018-09-29 15:54:47] RB7_A2: plotting length histogram INFO [2018-09-29 15:54:48] RB7_D3: creating output directory:.//RB7_D3 INFO [2018-09-29 15:54:48] RB7_D3: summarising input file for flowcell INFO [2018-09-29 15:54:49] RB7_D3: plotting length histogram INFO [2018-09-29 15:54:49] RB7_A2: plotting mean Q score histogram INFO [2018-09-29 15:54:52] RB7_A2: plotting flowcell overview INFO [2018-09-29 15:54:52] RB7_D3: plotting mean Q score histogram INFO [2018-09-29 15:54:55] RB7_D3: plotting flowcell overview INFO [2018-09-29 15:55:24] RB7_A2: plotting flowcell yield over time INFO [2018-09-29 15:55:30] RB7_A2: plotting flowcell yield by read length INFO [2018-09-29 15:55:34] RB7_D3: plotting flowcell yield over time INFO [2018-09-29 15:55:35] RB7_A2: plotting sequence length over time INFO [2018-09-29 15:55:41] RB7_D3: plotting flowcell yield by read length INFO [2018-09-29 15:55:46] RB7_D3: plotting sequence length over time INFO [2018-09-29 15:55:48] Analysing data from all flowcells combined Error in rbindlist(results) : Item 1 of list input is not a data.frame, data.table or list Calls: as.data.frame -> rbindlist Execution halted

Could you please tell me what's the problem, and how can i fix this? Thank so much! Sincerely.

roblanf commented 6 years ago

Hi,

Can you double check that you are using the latest version from github? When I run the same command (perhaps obviously!) I don't get this error.

A few more questions:

  1. Can you check the output that you get for the single flowcells. Is it all there? Based on your commandline, it should be there in two folders (RB7_A2 and RB7_D3) in the directory you run the script from. The output should be identical to that in the example_output file.
  2. Can you tell me your OS details?

Thanks,

Rob