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Teichlab / cellphonedb

MIT License
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Issue with running the code #222

Closed dianadom closed 3 years ago

dianadom commented 3 years ago

Hi, I am running a code on a big files. Files with counts have 7GB.

The command which I am running is following: cellphonedb method statistical_analysis metadata.txt counts.txt --iterations=10 --project-name=new

This is a 'head' of metadata file:

Cell cell_type N7.EpiA.AAACATACACACTG TA_1 N7.EpiA.AAACCGTGCATCAG TA_1 N7.EpiA.AAACGCACAATCGC TA_2 N7.EpiA.AAAGATCTAACCGT Enterocyte_Progenitors N7.EpiA.AAAGATCTAGGCGA Enterocyte_Progenitors ....

and this is a 'head' of counts file: Gene N7.EpiA.AAACATACACACTG N7.EpiA.AAACCGTGCATCAG N7.EpiA.AAACGCACAATCGC N7.EpiA.AAAGATCTAACCGT N7.EpiA.AAAGATCTAGGCGN7.EpiA.AAAGCCTGCTCGAA N7.EpiA.AAATCAACATCACG N7.EpiA.AAATCAACCTTGGA N7.EpiA.AAATCATGGAAAGT N7.EpiA.AAATCCCTCACTTT N7.EpiA.AACAAACTGTATGC N7.EpiA.AACAAACTTCTCCG ..... 7SK 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.592989170245371 0 0 0 0 0 0 0 0 0 0 0 0 0 1.80225274494389 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.67952384541575 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3.08145210306442 0 0..... A1BG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.2072425502065 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.690259738916243 0 0 0 0 0 0 0 0 0 0 0 0 0 0.738263600026138 0 0 0 0 0 0 0 0 0 0 0 0 0 0.519176176574229 0 0 0 0 0 0 0 0 0 0 0 0 0 0.481101840353243 0 0 0 0 0 0 0 0 0 0 0 0 0 0.651909543708293 0 0...... ....

After running the command I am getting the following information: [ ][APP][13/11/20-09:46:24][WARNING] Latest local available version is v2.0.0, using it [ ][APP][13/11/20-09:46:24][WARNING] User selected downloaded database v2.0.0 is available, using it [ ][CORE][13/11/20-09:46:24][INFO] Initializing SqlAlchemy CellPhoneDB Core [ ][CORE][13/11/20-09:46:24][INFO] Using custom database at /cluster/home/dianadom/.cpdb/releases/v2.0.0/cellphone.db [ ][APP][13/11/20-09:46:24][INFO] Launching Method cpdb_statistical_analysis_local_method_launcher [ ][APP][13/11/20-09:46:24][INFO] Launching Method _set_paths [ ][APP][13/11/20-09:46:24][INFO] Launching Method _load_meta_counts

After it the job is not running anymore ( no information that it has been killed) and I am not getting any output.

edwardkim1 commented 3 years ago

I have the same issue here using the test data. The job does not run after "Launching Method _counts_validations" and Ctrl+C is unable to kill it either.

madelarambelje commented 3 years ago

I am having this problem as well, can this be caused due to the lack of computational power or memory?

prete commented 3 years ago

Hi @dianadom @edwardkim1 @madelarambelje this sounds like it could be a memory issue. Could you try upgrading to the beta version of CellPhoneDB (pip install -U CellPhoneDB==2.1.8b3) and see if you're still facing this issue?

Similar to #282

madelarambelje commented 3 years ago

It was indeed a memory issue. It's running smoothly now. Thanks for responding!