search

tzcoolman / FACS-OLD

0 stars 2 forks source link

Statistics does not match output - simple_remove #16

Closed henrikstranneheim closed 12 years ago

henrikstranneheim commented 12 years ago

Processed: ./DRASS/simple_remove -t 0.8 -q datasets/SimHC-454.7b8911bf.fna -r bloomfilters/henriks/Sim_HC/21_0.005/E_coli.bloom -o analysis/henriks/Sim_HC/21_0.005/

Out: all_ref->bloomfilters/henriks/Sim_HC/21_0.005/E_coli.bloom distributing... task->6043466 bloom name->bloomfilters/henriks/Sim_HC/21_0.005/E_coli.bloom successful bloom read... fasta processing... fasta processing... fasta processing... fasta processing... all->0 contam->0 fasta processing... all->0 contam->0 fasta processing... all->0 contam->0 fasta processing... all->0 contam->0 fasta processing... all->0 contam->0 all->0 contam->0 all->12478 contam->1672 all->87522 contam->4 saving... match->analysis/henriks/Sim_HC/21_0.005/SimHC-454.7b8911bf_contam_E_coli.fasta mis->analysis/henriks/Sim_HC/21_0.005/SimHC-454.7b8911bf_clean_E_coli.fasta finish processing... total=5 sec

grep Esc analysis/henriks/Sim_HC/21_0.005/SimHC-454.7b8911bf_contam_E_coli.fasta | wc -l 2834 [henriks@kalkyl1 private]$ grep ">" analysis/henriks/Sim_HC/21_0.005/SimHC-454.7b8911bf_contam_E_coli.fasta | wc -l 13861 [henriks@kalkyl1 private]$ grep Homo analysis/henriks/Sim_HC/21_0.005/SimHC-454.7b8911bf_contam_E_coli.fasta | wc -l 8962

tzcoolman commented 12 years ago

Let have a test and get back to ya

tzcoolman commented 12 years ago

I have tested 'simple_remove' both on UPPMAX and on my machine... Both have generated the correct result. I dont know what was going on when you were testing it? So plz show me this on Monday...

henrikstranneheim commented 12 years ago

Strange, when I process as before I get the same incorrect results. However, when I delete all files and process again I get a "correct" result. Processing several times, without deleting in between now yields a correct result.

Weird but well, all seems fine now..

Henrik Stranneheim Ph.D. Department of Molecular Medicine and Surgery Karolinska Institute Science for Life Laboratory, KISP SE-171 65 Solna, Sweden

E-mail: henrik.stranneheim@scilifelab.se Phone: +46 (0)8 524 81487 (Office) Phone: +46 (0)736251487 (Mobile) Visiting address: Tometebodavägen 23A

On 9 sep 2012, at 11:06, tzcoolman wrote:

I have tested 'simple_remove' both on UPPMAX and on my machine... Both have generated the correct result. I dont know what was going on when you were testing it? So plz show me this on Monday...

— Reply to this email directly or view it on GitHub.