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CRISPRlab / CRISPRdisco

CRISPR discovery pipeline
GNU General Public License v2.0
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./test.sh shows some differences #6

Closed YanpingHu closed 4 years ago

YanpingHu commented 5 years ago

After I run ./test.sh,the result shows: _diff -s test/known_results/CRISPR-Cas_Subtype_summary.csv test/test_output/CRISPR-Cas_Subtype_summary.csv 3c3 < 1,TypeI-B,2

1,TypeI-B,0 9c9 < 7,TypeII-A,1

7,TypeII-A,0 diff -s test/known_results/CRISPR-Cas_Type_summary.csv test/test_output/CRISPR-Cas_Type_summary.csv 2,3c2,3 < 0,TypeI,2 < 1,TypeII,1

0,TypeI,0 1,TypeII,0 diff -s test/known_results/CRISPR_repeat_seqs_TEST.csv test/test_output/CRISPR_repeat_seqs_TEST.csv 2,4c2,4 < 0,NC_006449,minced:0.2.0,repeat_unit,625101,627844,42,+,CRISPR1,TTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC < 0,NC_023011,minced:0.2.0,repeat_unit,98414,99292,14,+,CRISPR1,TTTCAGACGAACCCTCGTGGGGTTGAAGC < 0,NC_015847,minced:0.2.0,repeat_unit,1030344,1034394,56,-,CRISPR1,GTTTCAATGCTTGTTATTTTGCAAGTTATTCTTTTA

0,NC_006449,minced:0.2.0,repeat_unit,627809,627844,42,+,CRISPR1,TTTTTGTACTCTCAAGATTTAAGTAACTGTACAAC 0,NC_023011,minced:0.2.0,repeat_unit,99263,99292,14,+,CRISPR1,TTTCAGACGAACCCTCGTGGGGTTGAAGC 0,NC_015847,minced:0.2.0,repeat_unit,1034358,1034394,56,-,CRISPR1,GTTTCAATGCTTGTTATTTTGCAAGTTATTCTTTTA Files test/known_results/Genomes_without_CRISPR_TEST.csv and test/test_output/Genomes_without_CRISPR_TEST.csv are identical Files test/known_results/.gitignore and test/test_output/.gitignore are identical diff -s test/known_results/Master_CRISPR_summary_table_TEST.csv test/test_output/Master_CRISPR_summary_table_TEST.csv 2,4c2,4 < 0,NC_006449,1.0,6.0,6.0,cas1|cas9|csm6|csn2,TypeII,TypeII-A,1,0,0, < 1,NC_015847,1.0,4.0,4.0,cas1|cas3|cas4|cas8b,TypeI,TypeI-B,1,0,0, < 2,NC_023011,1.0,4.0,4.0,cas1|cas3|cas4|cas8b,TypeI,TypeI-B,1,0,0,

0,NC_006449,1.0,0.0,0.0,0,0,0,0,0,0, 1,NC_015847,1.0,0.0,0.0,0,0,0,0,0,0, 2,NC_023011,1.0,0.0,0.0,0,0,0,0,0,0, Files test/known_results/repeat_summary_table_TEST.csv and test/test_output/repeat_summary_table_TEST.csv are identical

I help you help me to solve it.Thanks

abriner commented 5 years ago

Hi YanpingHu - It doesn't look like the blast ran. Are you using the program in the docker container or did you install it locally?

If you installed it locally, you need to change the location of the reference data sets in the code and reinstall the program.

YanpingHu commented 4 years ago

I install it locally.Because I just started learning it,I don't know what should I do next.Could you tell me how to change the location of the reference data sets in the code.Thanks!

abriner commented 4 years ago

See this section on the README. Screen Shot 2019-11-11 at 9 25 44 AM