Commit ede49e8f authored by peguerin's avatar peguerin
Browse files

file rapidrun

parent 0fdf73bb
# snakemake_rapidrun_swarm
OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
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OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
# Prerequisites
pip3 install pymysql
pip install pandas
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P1_A1 180430_SN234_A_L001_AIMI-9 SPY173250 Guadeloupe chond
P1_B1 180430_SN234_A_L001_AIMI-9 SPY173251 Guadeloupe chond
P1_C1 180430_SN234_A_L001_AIMI-9 SPY173252 Guadeloupe chond
P1_D1 180430_SN234_A_L001_AIMI-9 SPY173253 Guadeloupe chond
P1_E1 180430_SN234_A_L001_AIMI-9 SPY173254 Guadeloupe chond
P1_F1 180430_SN234_A_L001_AIMI-9 SPY173255 Guadeloupe chond
P1_G1 180430_SN234_A_L001_AIMI-9 SPY173256 Guadeloupe chond
P1_H1 180430_SN234_A_L001_AIMI-9 SPY173257 Guadeloupe chond
P1_A3 180430_SN234_A_L001_AIMI-9 SPY173258 Guadeloupe chond
P1_B3 180430_SN234_A_L001_AIMI-9 SPY173259 Guadeloupe chond
P1_A1 180504_SND405_A_L001_AIMI-10 SPY173260 Guadeloupe chond
P1_B1 180504_SND405_A_L001_AIMI-10 SPY173261 Guadeloupe chond
P1_C1 180504_SND405_A_L001_AIMI-10 SPY173262 Guadeloupe chond
P1_D1 180504_SND405_A_L001_AIMI-10 SPY173263 Guadeloupe chond
P1_E1 180504_SND405_A_L001_AIMI-10 SPY173264 Guadeloupe chond
P1_F1 180504_SND405_A_L001_AIMI-10 SPY173265 Guadeloupe chond
P1_G1 180504_SND405_A_L001_AIMI-10 SPY173266 Guadeloupe chond
P1_H1 180504_SND405_A_L001_AIMI-10 SPY173267 Guadeloupe chond
P1_A3 180504_SND405_A_L001_AIMI-10 SPY173268 Guadeloupe chond
P1_B3 180504_SND405_A_L001_AIMI-10 SPY173269 Guadeloupe chond
P1_C3 180504_SND405_A_L001_AIMI-10 SPY173270 Guadeloupe chond
P1_D3 180504_SND405_A_L001_AIMI-10 SPY173271 Guadeloupe chond
P1_H3 180504_SND405_A_L002_AIMI-11 SPY173272 Guadeloupe chond
P1_A5 180504_SND405_A_L002_AIMI-11 SPY180501 Guadeloupe chond
P1_B5 180504_SND405_A_L002_AIMI-11 SPY173273 Guadeloupe chond
P1_C5 180504_SND405_A_L002_AIMI-11 SPY173274 Guadeloupe chond
P1_D5 180504_SND405_A_L002_AIMI-11 SPY173275 Guadeloupe chond
P1_E5 180504_SND405_A_L002_AIMI-11 SPY173276 Guadeloupe chond
P1_F5 180504_SND405_A_L002_AIMI-11 SPY173278 Guadeloupe chond
P1_G5 180504_SND405_A_L002_AIMI-11 SPY173279 Guadeloupe chond
P1_H5 180504_SND405_A_L002_AIMI-11 SPY173280 Guadeloupe chond
P1_A7 180504_SND405_A_L002_AIMI-11 SPY173281 Guadeloupe chond
P1_B7 180504_SND405_A_L002_AIMI-11 SPY173282 Guadeloupe chond
P1_C7 180504_SND405_A_L002_AIMI-11 SPY173283 Guadeloupe chond
P1_A1 181102_SND405_A_L001_AIMI-48 SPY181533 Fakarava chond
P1_B1 181102_SND405_A_L001_AIMI-48 SPY181536 Fakarava chond
P1_C1 181102_SND405_A_L001_AIMI-48 SPY181541 Fakarava chond
P1_D1 181102_SND405_A_L001_AIMI-48 SPY181831 Fakarava chond
P1_E1 181102_SND405_A_L001_AIMI-48 SPY181832 Fakarava chond
P1_F1 181102_SND405_A_L001_AIMI-48 SPY181885 Fakarava chond
P1_G1 181102_SND405_A_L001_AIMI-48 SPY181886 Fakarava chond
P1_H1 181102_SND405_A_L001_AIMI-48 SPY181887 Fakarava chond
P1_A3 181102_SND405_A_L001_AIMI-48 SPY181888 Fakarava chond
P1_B3 181102_SND405_A_L001_AIMI-48 SPY181892 Fakarava chond
P1_D3 181102_SND405_A_L001_AIMI-48 SPY181895 Fakarava chond
P1_E3 181102_SND405_A_L001_AIMI-48 SPY181896 Fakarava chond
P1_F3 181102_SND405_A_L001_AIMI-48 SPY181899 Fakarava chond
P1_G3 181102_SND405_A_L001_AIMI-48 SPY181900 Fakarava chond
P1_H3 181102_SND405_A_L001_AIMI-48 SPY181902 Fakarava chond
P1_A5 181102_SND405_A_L001_AIMI-48 SPY181905 Fakarava chond
P1_B5 181102_SND405_A_L001_AIMI-48 SPY181906 Fakarava chond
P1_C5 181102_SND405_A_L001_AIMI-48 SPY181907 Fakarava chond
P1_D5 181102_SND405_A_L001_AIMI-48 SPY181909 Fakarava chond
P1_E5 181102_SND405_A_L001_AIMI-48 SPY181911 Fakarava chond
P1_F5 181102_SND405_A_L001_AIMI-48 SPY181912 Fakarava chond
P1_G5 181102_SND405_A_L001_AIMI-48 SPY181914 Fakarava chond
P1_H5 181102_SND405_A_L001_AIMI-48 SPY181915 Fakarava chond
P1_A7 181102_SND405_A_L001_AIMI-48 SPY181917 Fakarava chond
P1_B7 181102_SND405_A_L001_AIMI-48 SPY181918 Fakarava chond
P1_C7 181102_SND405_A_L001_AIMI-48 SPY181919 Fakarava chond
P1_D7 181102_SND405_A_L001_AIMI-48 SPY181920 Fakarava chond
P1_E7 181102_SND405_A_L001_AIMI-48 SPY181922 Fakarava chond
P1_D1 181102_SND405_A_L002_AIMI-49 SPY180581 Malpelo chond
P1_E1 181102_SND405_A_L002_AIMI-49 SPY180582 Malpelo chond
P1_F1 181102_SND405_A_L002_AIMI-49 SPY180583 Malpelo chond
P1_G1 181102_SND405_A_L002_AIMI-49 SPY180584 Malpelo chond
P1_H1 181102_SND405_A_L002_AIMI-49 SPY180585 Malpelo chond
P1_A3 181102_SND405_A_L002_AIMI-49 SPY180586 Malpelo chond
P1_B3 181102_SND405_A_L002_AIMI-49 SPY180587 Malpelo chond
P1_C3 181102_SND405_A_L002_AIMI-49 SPY180588 Malpelo chond
P1_D3 181102_SND405_A_L002_AIMI-49 SPY180589 Malpelo chond
P1_E3 181102_SND405_A_L002_AIMI-49 SPY180590 Malpelo chond
P1_F3 181102_SND405_A_L002_AIMI-49 SPY180591 Malpelo chond
P1_G3 181102_SND405_A_L002_AIMI-49 SPY180592 Malpelo chond
P1_H3 181102_SND405_A_L002_AIMI-49 SPY180593 Malpelo chond
P1_A5 181102_SND405_A_L002_AIMI-49 SPY180594 Malpelo chond
P1_B5 181102_SND405_A_L002_AIMI-49 SPY180595 Malpelo chond
P1_C5 181102_SND405_A_L002_AIMI-49 SPY180596 Malpelo chond
P1_D5 181102_SND405_A_L002_AIMI-49 SPY180597 Malpelo chond
P1_E5 181102_SND405_A_L002_AIMI-49 SPY180598 Malpelo chond
P1_G5 181102_SND405_A_L002_AIMI-49 SPY180599 Malpelo chond
P1_H5 181102_SND405_A_L002_AIMI-49 SPY180600 Malpelo chond
P1_A7 181102_SND405_A_L002_AIMI-49 SPY180601 Malpelo chond
P1_B7 181102_SND405_A_L002_AIMI-49 SPY180602 Malpelo chond
P1_C7 181102_SND405_A_L002_AIMI-49 SPY180603 Malpelo chond
P1_D7 181102_SND405_A_L002_AIMI-49 SPY180604 Malpelo chond
P1_E7 181102_SND405_A_L002_AIMI-49 SPY180605 Malpelo chond
P1_F7 181102_SND405_A_L002_AIMI-49 SPY180768 Malpelo chond
P1_A1 181116_SND405_A_L001_AIMI-50 SPY180769 Malpelo chond
P1_B1 181116_SND405_A_L001_AIMI-50 SPY180773 Malpelo chond
P1_C1 181116_SND405_A_L001_AIMI-50 SPY180775 Malpelo chond
P1_D1 181116_SND405_A_L001_AIMI-50 SPY180776 Malpelo chond
P1_E1 181116_SND405_A_L001_AIMI-50 SPY180777 Malpelo chond
P1_F1 181116_SND405_A_L001_AIMI-50 SPY180778 Malpelo chond
P1_G1 181116_SND405_A_L001_AIMI-50 SPY180779 Malpelo chond
P1_H1 181116_SND405_A_L001_AIMI-50 SPY180780 Malpelo chond
P1_A3 181116_SND405_A_L001_AIMI-50 SPY180781 Malpelo chond
P1_B3 181116_SND405_A_L001_AIMI-50 SPY180782 Malpelo chond
P1_A1 181102_SND405_A_L001_AIMI-48 SPY181533 Fakarava mamm
P1_B1 181102_SND405_A_L001_AIMI-48 SPY181536 Fakarava mamm
P1_C1 181102_SND405_A_L001_AIMI-48 SPY181541 Fakarava mamm
P1_D1 181102_SND405_A_L001_AIMI-48 SPY181831 Fakarava mamm
P1_E1 181102_SND405_A_L001_AIMI-48 SPY181832 Fakarava mamm
P1_F1 181102_SND405_A_L001_AIMI-48 SPY181885 Fakarava mamm
P1_G1 181102_SND405_A_L001_AIMI-48 SPY181886 Fakarava mamm
P1_H1 181102_SND405_A_L001_AIMI-48 SPY181887 Fakarava mamm
P1_A3 181102_SND405_A_L001_AIMI-48 SPY181888 Fakarava mamm
P1_B3 181102_SND405_A_L001_AIMI-48 SPY181892 Fakarava mamm
P1_D3 181102_SND405_A_L001_AIMI-48 SPY181895 Fakarava mamm
P1_E3 181102_SND405_A_L001_AIMI-48 SPY181896 Fakarava mamm
P1_F3 181102_SND405_A_L001_AIMI-48 SPY181899 Fakarava mamm
P1_G3 181102_SND405_A_L001_AIMI-48 SPY181900 Fakarava mamm
P1_H3 181102_SND405_A_L001_AIMI-48 SPY181902 Fakarava mamm
P1_A5 181102_SND405_A_L001_AIMI-48 SPY181905 Fakarava mamm
P1_B5 181102_SND405_A_L001_AIMI-48 SPY181906 Fakarava mamm
P1_C5 181102_SND405_A_L001_AIMI-48 SPY181907 Fakarava mamm
P1_D5 181102_SND405_A_L001_AIMI-48 SPY181909 Fakarava mamm
P1_E5 181102_SND405_A_L001_AIMI-48 SPY181911 Fakarava mamm
P1_F5 181102_SND405_A_L001_AIMI-48 SPY181912 Fakarava mamm
P1_G5 181102_SND405_A_L001_AIMI-48 SPY181914 Fakarava mamm
P1_H5 181102_SND405_A_L001_AIMI-48 SPY181915 Fakarava mamm
P1_B7 181102_SND405_A_L001_AIMI-48 SPY181917 Fakarava mamm
P1_C7 181102_SND405_A_L001_AIMI-48 SPY181918 Fakarava mamm
P1_D7 181102_SND405_A_L001_AIMI-48 SPY181919 Fakarava mamm
P1_E7 181102_SND405_A_L001_AIMI-48 SPY181920 Fakarava mamm
P1_F7 181102_SND405_A_L001_AIMI-48 SPY181922 Fakarava mamm
P1_A1 181102_SND405_A_L002_AIMI-49 SPY180581 Malpelo mamm
P1_B1 181102_SND405_A_L002_AIMI-49 SPY180582 Malpelo mamm
P1_C1 181102_SND405_A_L002_AIMI-49 SPY180583 Malpelo mamm
P1_D1 181102_SND405_A_L002_AIMI-49 SPY180584 Malpelo mamm
P1_E1 181102_SND405_A_L002_AIMI-49 SPY180585 Malpelo mamm
P1_F1 181102_SND405_A_L002_AIMI-49 SPY180586 Malpelo mamm
P1_G1 181102_SND405_A_L002_AIMI-49 SPY180587 Malpelo mamm
P1_H1 181102_SND405_A_L002_AIMI-49 SPY180588 Malpelo mamm
P1_A3 181102_SND405_A_L002_AIMI-49 SPY180589 Malpelo mamm
P1_B3 181102_SND405_A_L002_AIMI-49 SPY180590 Malpelo mamm
P1_C3 181102_SND405_A_L002_AIMI-49 SPY180591 Malpelo mamm
P1_D3 181102_SND405_A_L002_AIMI-49 SPY180592 Malpelo mamm
P1_E3 181102_SND405_A_L002_AIMI-49 SPY180593 Malpelo mamm
P1_F3 181102_SND405_A_L002_AIMI-49 SPY180594 Malpelo mamm
P1_G3 181102_SND405_A_L002_AIMI-49 SPY180595 Malpelo mamm
P1_H3 181102_SND405_A_L002_AIMI-49 SPY180596 Malpelo mamm
P1_A5 181102_SND405_A_L002_AIMI-49 SPY180597 Malpelo mamm
P1_B5 181102_SND405_A_L002_AIMI-49 SPY180598 Malpelo mamm
P1_D5 181102_SND405_A_L002_AIMI-49 SPY180599 Malpelo mamm
P1_E5 181102_SND405_A_L002_AIMI-49 SPY180600 Malpelo mamm
P1_F5 181102_SND405_A_L002_AIMI-49 SPY180601 Malpelo mamm
P1_G5 181102_SND405_A_L002_AIMI-49 SPY180602 Malpelo mamm
P1_A7 181102_SND405_A_L002_AIMI-49 SPY180603 Malpelo mamm
P1_B7 181102_SND405_A_L002_AIMI-49 SPY180604 Malpelo mamm
P1_C7 181102_SND405_A_L002_AIMI-49 SPY180605 Malpelo mamm
P1_D7 181102_SND405_A_L002_AIMI-49 SPY180768 Malpelo mamm
P1_E7 181102_SND405_A_L002_AIMI-49 SPY180769 Malpelo mamm
P1_F7 181102_SND405_A_L002_AIMI-49 SPY180773 Malpelo mamm
P1_G7 181102_SND405_A_L002_AIMI-49 SPY180775 Malpelo mamm
P1_H7 181102_SND405_A_L002_AIMI-49 SPY180776 Malpelo mamm
P1_A9 181102_SND405_A_L002_AIMI-49 SPY180777 Malpelo mamm
P1_B9 181102_SND405_A_L002_AIMI-49 SPY180778 Malpelo mamm
P1_C9 181102_SND405_A_L002_AIMI-49 SPY180779 Malpelo mamm
P1_D9 181102_SND405_A_L002_AIMI-49 SPY180780 Malpelo mamm
P1_E9 181102_SND405_A_L002_AIMI-49 SPY180781 Malpelo mamm
P1_F9 181102_SND405_A_L002_AIMI-49 SPY180782 Malpelo mamm
This diff is collapsed.
P1_A1 181102_SND405_A_L001_AIMI-48 SPY181533 Fakarava vert
P1_B1 181102_SND405_A_L001_AIMI-48 SPY181536 Fakarava vert
P1_C1 181102_SND405_A_L001_AIMI-48 SPY181541 Fakarava vert
P1_D1 181102_SND405_A_L001_AIMI-48 SPY181831 Fakarava vert
P1_E1 181102_SND405_A_L001_AIMI-48 SPY181832 Fakarava vert
P1_F1 181102_SND405_A_L001_AIMI-48 SPY181885 Fakarava vert
P1_G1 181102_SND405_A_L001_AIMI-48 SPY181886 Fakarava vert
P1_H1 181102_SND405_A_L001_AIMI-48 SPY181887 Fakarava vert
P1_A3 181102_SND405_A_L001_AIMI-48 SPY181888 Fakarava vert
P1_B3 181102_SND405_A_L001_AIMI-48 SPY181892 Fakarava vert
P1_D3 181102_SND405_A_L001_AIMI-48 SPY181895 Fakarava vert
P1_E3 181102_SND405_A_L001_AIMI-48 SPY181896 Fakarava vert
P1_F3 181102_SND405_A_L001_AIMI-48 SPY181899 Fakarava vert
P1_G3 181102_SND405_A_L001_AIMI-48 SPY181900 Fakarava vert
P1_H3 181102_SND405_A_L001_AIMI-48 SPY181902 Fakarava vert
P1_A5 181102_SND405_A_L001_AIMI-48 SPY181905 Fakarava vert
P1_B5 181102_SND405_A_L001_AIMI-48 SPY181906 Fakarava vert
P1_C5 181102_SND405_A_L001_AIMI-48 SPY181907 Fakarava vert
P1_D5 181102_SND405_A_L001_AIMI-48 SPY181909 Fakarava vert
P1_E5 181102_SND405_A_L001_AIMI-48 SPY181911 Fakarava vert
P1_F5 181102_SND405_A_L001_AIMI-48 SPY181912 Fakarava vert
P1_G5 181102_SND405_A_L001_AIMI-48 SPY181914 Fakarava vert
P1_H5 181102_SND405_A_L001_AIMI-48 SPY181915 Fakarava vert
P1_A7 181102_SND405_A_L001_AIMI-48 SPY181917 Fakarava vert
P1_B7 181102_SND405_A_L001_AIMI-48 SPY181918 Fakarava vert
P1_C7 181102_SND405_A_L001_AIMI-48 SPY181919 Fakarava vert
P1_D7 181102_SND405_A_L001_AIMI-48 SPY181920 Fakarava vert
P1_E7 181102_SND405_A_L001_AIMI-48 SPY181922 Fakarava vert
P1_A3 181116_SND405_A_L001_AIMI-50 SPY180581 Malpelo vert
P1_B3 181116_SND405_A_L001_AIMI-50 SPY180582 Malpelo vert
P1_C3 181116_SND405_A_L001_AIMI-50 SPY180583 Malpelo vert
P1_D3 181116_SND405_A_L001_AIMI-50 SPY180584 Malpelo vert
P1_E3 181116_SND405_A_L001_AIMI-50 SPY180585 Malpelo vert
P1_F3 181116_SND405_A_L001_AIMI-50 SPY180586 Malpelo vert
P1_G3 181116_SND405_A_L001_AIMI-50 SPY180587 Malpelo vert
P1_H3 181116_SND405_A_L001_AIMI-50 SPY180588 Malpelo vert
P1_A5 181116_SND405_A_L001_AIMI-50 SPY180589 Malpelo vert
P1_B5 181116_SND405_A_L001_AIMI-50 SPY180590 Malpelo vert
P1_C5 181116_SND405_A_L001_AIMI-50 SPY180591 Malpelo vert
P1_D5 181116_SND405_A_L001_AIMI-50 SPY180592 Malpelo vert
P1_E5 181116_SND405_A_L001_AIMI-50 SPY180593 Malpelo vert
P1_F5 181116_SND405_A_L001_AIMI-50 SPY180594 Malpelo vert
P1_G5 181116_SND405_A_L001_AIMI-50 SPY180595 Malpelo vert
P1_H5 181116_SND405_A_L001_AIMI-50 SPY180596 Malpelo vert
P1_A7 181116_SND405_A_L001_AIMI-50 SPY180597 Malpelo vert
P1_B7 181116_SND405_A_L001_AIMI-50 SPY180598 Malpelo vert
P1_A1 181116_SND405_A_L002_AIMI-51 SPY180599 Malpelo vert
P1_B1 181116_SND405_A_L002_AIMI-51 SPY180600 Malpelo vert
P1_C1 181116_SND405_A_L002_AIMI-51 SPY180601 Malpelo vert
P1_D1 181116_SND405_A_L002_AIMI-51 SPY180602 Malpelo vert
P1_E1 181116_SND405_A_L002_AIMI-51 SPY180603 Malpelo vert
P1_F1 181116_SND405_A_L002_AIMI-51 SPY180604 Malpelo vert
P1_G1 181116_SND405_A_L002_AIMI-51 SPY180605 Malpelo vert
P1_H1 181116_SND405_A_L002_AIMI-51 SPY180768 Malpelo vert
P1_A3 181116_SND405_A_L002_AIMI-51 SPY180769 Malpelo vert
P1_B3 181116_SND405_A_L002_AIMI-51 SPY180773 Malpelo vert
P1_C3 181116_SND405_A_L002_AIMI-51 SPY180775 Malpelo vert
P1_D3 181116_SND405_A_L002_AIMI-51 SPY180776 Malpelo vert
P1_E3 181116_SND405_A_L002_AIMI-51 SPY180777 Malpelo vert
P1_F3 181116_SND405_A_L002_AIMI-51 SPY180778 Malpelo vert
P1_G3 181116_SND405_A_L002_AIMI-51 SPY180779 Malpelo vert
P1_H3 181116_SND405_A_L002_AIMI-51 SPY180780 Malpelo vert
P1_A5 181116_SND405_A_L002_AIMI-51 SPY180781 Malpelo vert
P1_B5 181116_SND405_A_L002_AIMI-51 SPY180782 Malpelo vert
This diff is collapsed.
teleo,ACACCGCCCGTCACTCT,CTTCCGGTACACTTACCATG
vert,TAGAACAGGCTCCTCTAG,TTAGATACCCCACTATGC
chond,ACACCGCCCGTCACTCTC,CATGTTACGACTTGCCTCCTC
mamm,CCGCCCGTCACYCTCCT,GTAYRCTTACCWTGTTACGAC
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