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annotate test-data/staramr/settings.txt @ 0:a157d29ef11d draft default tip

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planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
author pimarin
date Mon, 15 May 2023 14:20:18 +0000
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a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
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1 command_line = /home/piemari/apps/conda/envs/amr/bin/staramr search --nprocs 4 --no-exclude-genes --pid-threshold 95 --percent-length-overlap-resfinder 90 --percent-length-overlap-pointfinder 90 --percent-length-overlap-plasmidfinder 90 --output-dir /storage/scratch/piemari/60579242/staramr/staramr_10_Enterococcus_faecalis_S17_L001 /storage/scratch/piemari/60579242/staramr/10_Enterococcus_faecalis_S17_L001.fasta
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
pimarin
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2 version = 0.9.1
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3 start_time = 2023-02-13 14:26:11
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4 end_time = 2023-02-13 14:26:13
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5 total_minutes = 0.04
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6 resfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/resfinder
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
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7 resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git
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8 resfinder_db_commit = 23661dbb58797b302464855611223b7ba4a21f75
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
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9 resfinder_db_date = Fri, 02 Dec 2022 11:36
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10 pointfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/pointfinder
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11 pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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12 pointfinder_db_commit = a25ac32c7a7a904dff14ffbd17e3b3f7cd732954
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13 pointfinder_db_date = Fri, 28 Oct 2022 10:19
a157d29ef11d planemo upload commit 4b30072ce6fff8554976af6fb4fce92069d39a6e
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14 pointfinder_organisms_all = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, klebsiella, mycobacterium_tuberculosis, neisseria_gonorrhoeae, plasmodium_falciparum, salmonella, staphylococcus_aureus
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15 pointfinder_organisms_valid = campylobacter, enterococcus_faecalis, enterococcus_faecium, escherichia_coli, helicobacter_pylori, salmonella
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16 plasmidfinder_db_dir = /home/piemari/apps/conda/envs/amr/lib/python3.11/site-packages/staramr/databases/data/update/plasmidfinder
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17 plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
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18 plasmidfinder_db_commit = b1c9ddac0e618e07630a94452293d84f296a6de5
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19 plasmidfinder_db_date = Thu, 12 Jan 2023 12:51
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20 mlst_version = 2.23.0
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21 pointfinder_organism = None
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22 pointfinder_gene_drug_version = 072621.1
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23 resfinder_gene_drug_version = 072621