cd /N/dc2/projects/marinovg/2015-07-17-assembly-contamination-check; python /N/dc2/projects/marinovg/programs/SPAdes-3.5.0-Linux/bin/spades.py --pe1-1 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M12/Sample_M12.forward_paired.fq --pe2-1 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M12/Sample_M12.reverse_paired.fq --pe1-2 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M13/Sample_M13.forward_paired.fq --pe2-2 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M13/Sample_M13.reverse_paired.fq --pe1-3 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M14/Sample_M14.forward_paired.fq --pe2-3 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M14/Sample_M14.reverse_paired.fq --pe1-4 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M15/Sample_M15.forward_paired.fq --pe2-4 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M15/Sample_M15.reverse_paired.fq --pe1-5 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M17/Sample_M17.forward_paired.fq --pe2-5 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M17/Sample_M17.reverse_paired.fq --pe1-6 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M18/Sample_M18.forward_paired.fq --pe2-6 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M18/Sample_M18.reverse_paired.fq --pe1-7 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M2/Sample_M2.forward_paired.fq --pe2-7 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M2/Sample_M2.reverse_paired.fq --pe1-8 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M20/Sample_M20.forward_paired.fq --pe2-8 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M20/Sample_M20.reverse_paired.fq --pe1-9 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M23/Sample_M23.forward_paired.fq --pe2-9 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M23/Sample_M23.reverse_paired.fq --pe1-10 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M24/Sample_M24.forward_paired.fq --pe2-10 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M24/Sample_M24.reverse_paired.fq --pe1-11 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M25/Sample_M25.forward_paired.fq --pe2-11 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M25/Sample_M25.reverse_paired.fq --pe1-12 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M26/Sample_M26.forward_paired.fq --pe2-12 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M26/Sample_M26.reverse_paired.fq --pe1-13 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M27/Sample_M27.forward_paired.fq --pe2-13 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M27/Sample_M27.reverse_paired.fq --pe1-14 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M28/Sample_M28.forward_paired.fq --pe2-14 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M28/Sample_M28.reverse_paired.fq --pe1-15 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M29/Sample_M29.forward_paired.fq --pe2-15 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M29/Sample_M29.reverse_paired.fq --pe1-16 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M3/Sample_M3.forward_paired.fq --pe2-16 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M3/Sample_M3.reverse_paired.fq --pe1-17 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M30/Sample_M30.forward_paired.fq --pe2-17 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M30/Sample_M30.reverse_paired.fq --pe1-18 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M31/Sample_M31.forward_paired.fq --pe2-18 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M31/Sample_M31.reverse_paired.fq --pe1-19 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M32/Sample_M32.forward_paired.fq --pe2-19 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M32/Sample_M32.reverse_paired.fq --pe1-20 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M33/Sample_M33.forward_paired.fq --pe2-20 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M33/Sample_M33.reverse_paired.fq --pe1-21 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M34/Sample_M34.forward_paired.fq --pe2-21 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M34/Sample_M34.reverse_paired.fq --pe1-22 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M35/Sample_M35.forward_paired.fq --pe2-22 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M35/Sample_M35.reverse_paired.fq --pe1-23 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M38/Sample_M38.forward_paired.fq --pe2-23 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M38/Sample_M38.reverse_paired.fq --pe1-24 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M4/Sample_M4.forward_paired.fq --pe2-24 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M4/Sample_M4.reverse_paired.fq --pe1-25 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M40/Sample_M40.forward_paired.fq --pe2-25 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M40/Sample_M40.reverse_paired.fq --pe1-26 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M41/Sample_M41.forward_paired.fq --pe2-26 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M41/Sample_M41.reverse_paired.fq --pe1-27 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M42/Sample_M42.forward_paired.fq --pe2-27 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M42/Sample_M42.reverse_paired.fq --pe1-28 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M43/Sample_M43.forward_paired.fq --pe2-28 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M43/Sample_M43.reverse_paired.fq --pe1-29 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M44/Sample_M44.forward_paired.fq --pe2-29 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M44/Sample_M44.reverse_paired.fq --pe1-30 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M46/Sample_M46.forward_paired.fq --pe2-30 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M46/Sample_M46.reverse_paired.fq --pe1-31 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M48/Sample_M48.forward_paired.fq --pe2-31 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M48/Sample_M48.reverse_paired.fq --pe1-32 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M5/Sample_M5.forward_paired.fq --pe2-32 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M5/Sample_M5.reverse_paired.fq --pe1-33 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M9/Sample_M9.forward_paired.fq --pe2-33 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150116/Sample_M9/Sample_M9.reverse_paired.fq --pe1-34 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M10/Sample_M10.forward_paired.fq --pe2-34 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M10/Sample_M10.reverse_paired.fq --pe1-35 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M12/Sample_M12.forward_paired.fq --pe2-35 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M12/Sample_M12.reverse_paired.fq --pe1-36 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M13/Sample_M13.forward_paired.fq --pe2-36 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M13/Sample_M13.reverse_paired.fq --pe1-37 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M14/Sample_M14.forward_paired.fq --pe2-37 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M14/Sample_M14.reverse_paired.fq --pe1-38 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M15/Sample_M15.forward_paired.fq --pe2-38 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M15/Sample_M15.reverse_paired.fq --pe1-39 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M17/Sample_M17.forward_paired.fq --pe2-39 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M17/Sample_M17.reverse_paired.fq --pe1-40 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M18/Sample_M18.forward_paired.fq --pe2-40 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M18/Sample_M18.reverse_paired.fq --pe1-41 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M2/Sample_M2.forward_paired.fq --pe2-41 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M2/Sample_M2.reverse_paired.fq --pe1-42 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M20/Sample_M20.forward_paired.fq --pe2-42 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M20/Sample_M20.reverse_paired.fq --pe1-43 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M23/Sample_M23.forward_paired.fq --pe2-43 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M23/Sample_M23.reverse_paired.fq --pe1-44 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M24/Sample_M24.forward_paired.fq --pe2-44 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M24/Sample_M24.reverse_paired.fq --pe1-45 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M25/Sample_M25.forward_paired.fq --pe2-45 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M25/Sample_M25.reverse_paired.fq --pe1-46 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M26/Sample_M26.forward_paired.fq --pe2-46 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M26/Sample_M26.reverse_paired.fq --pe1-47 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M27/Sample_M27.forward_paired.fq --pe2-47 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M27/Sample_M27.reverse_paired.fq --pe1-48 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M28/Sample_M28.forward_paired.fq --pe2-48 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M28/Sample_M28.reverse_paired.fq --pe1-49 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M29/Sample_M29.forward_paired.fq --pe2-49 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M29/Sample_M29.reverse_paired.fq --pe1-50 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M3/Sample_M3.forward_paired.fq --pe2-50 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M3/Sample_M3.reverse_paired.fq --pe1-51 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M30/Sample_M30.forward_paired.fq --pe2-51 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M30/Sample_M30.reverse_paired.fq --pe1-52 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M31/Sample_M31.forward_paired.fq --pe2-52 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M31/Sample_M31.reverse_paired.fq --pe1-53 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M32/Sample_M32.forward_paired.fq --pe2-53 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M32/Sample_M32.reverse_paired.fq --pe1-54 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M33/Sample_M33.forward_paired.fq --pe2-54 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M33/Sample_M33.reverse_paired.fq --pe1-55 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M34/Sample_M34.forward_paired.fq --pe2-55 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M34/Sample_M34.reverse_paired.fq --pe1-56 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M35/Sample_M35.forward_paired.fq --pe2-56 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M35/Sample_M35.reverse_paired.fq --pe1-57 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M38/Sample_M38.forward_paired.fq --pe2-57 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M38/Sample_M38.reverse_paired.fq --pe1-58 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M4/Sample_M4.forward_paired.fq --pe2-58 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M4/Sample_M4.reverse_paired.fq --pe1-59 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M40/Sample_M40.forward_paired.fq --pe2-59 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M40/Sample_M40.reverse_paired.fq --pe1-60 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M41/Sample_M41.forward_paired.fq --pe2-60 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M41/Sample_M41.reverse_paired.fq --pe1-61 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M42/Sample_M42.forward_paired.fq --pe2-61 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M42/Sample_M42.reverse_paired.fq --pe1-62 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M43/Sample_M43.forward_paired.fq --pe2-62 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M43/Sample_M43.reverse_paired.fq --pe1-63 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M46/Sample_M46.forward_paired.fq --pe2-63 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M46/Sample_M46.reverse_paired.fq --pe1-64 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M48/Sample_M48.forward_paired.fq --pe2-64 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M48/Sample_M48.reverse_paired.fq --pe1-65 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M5/Sample_M5.forward_paired.fq --pe2-65 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M5/Sample_M5.reverse_paired.fq --pe1-66 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M9/Sample_M9.forward_paired.fq --pe2-66 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150204/Sample_M9/Sample_M9.reverse_paired.fq --pe1-67 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M10/Sample_M10.forward_paired.fq --pe2-67 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M10/Sample_M10.reverse_paired.fq --pe1-68 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M12/Sample_M12.forward_paired.fq --pe2-68 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M12/Sample_M12.reverse_paired.fq --pe1-69 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M13/Sample_M13.forward_paired.fq --pe2-69 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M13/Sample_M13.reverse_paired.fq --pe1-70 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M14/Sample_M14.forward_paired.fq --pe2-70 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M14/Sample_M14.reverse_paired.fq --pe1-71 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M15/Sample_M15.forward_paired.fq --pe2-71 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M15/Sample_M15.reverse_paired.fq --pe1-72 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M17/Sample_M17.forward_paired.fq --pe2-72 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M17/Sample_M17.reverse_paired.fq --pe1-73 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M18/Sample_M18.forward_paired.fq --pe2-73 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M18/Sample_M18.reverse_paired.fq --pe1-74 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M2/Sample_M2.forward_paired.fq --pe2-74 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M2/Sample_M2.reverse_paired.fq --pe1-75 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M20/Sample_M20.forward_paired.fq --pe2-75 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M20/Sample_M20.reverse_paired.fq --pe1-76 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M23/Sample_M23.forward_paired.fq --pe2-76 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M23/Sample_M23.reverse_paired.fq --pe1-77 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M24/Sample_M24.forward_paired.fq --pe2-77 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M24/Sample_M24.reverse_paired.fq --pe1-78 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M25/Sample_M25.forward_paired.fq --pe2-78 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M25/Sample_M25.reverse_paired.fq --pe1-79 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M26/Sample_M26.forward_paired.fq --pe2-79 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M26/Sample_M26.reverse_paired.fq --pe1-80 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M27/Sample_M27.forward_paired.fq --pe2-80 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M27/Sample_M27.reverse_paired.fq --pe1-81 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M28/Sample_M28.forward_paired.fq --pe2-81 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M28/Sample_M28.reverse_paired.fq --pe1-82 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M29/Sample_M29.forward_paired.fq --pe2-82 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M29/Sample_M29.reverse_paired.fq --pe1-83 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M3/Sample_M3.forward_paired.fq --pe2-83 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M3/Sample_M3.reverse_paired.fq --pe1-84 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M30/Sample_M30.forward_paired.fq --pe2-84 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M30/Sample_M30.reverse_paired.fq --pe1-85 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M31/Sample_M31.forward_paired.fq --pe2-85 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M31/Sample_M31.reverse_paired.fq --pe1-86 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M32/Sample_M32.forward_paired.fq --pe2-86 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M32/Sample_M32.reverse_paired.fq --pe1-87 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M33/Sample_M33.forward_paired.fq --pe2-87 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M33/Sample_M33.reverse_paired.fq --pe1-88 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M34/Sample_M34.forward_paired.fq --pe2-88 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M34/Sample_M34.reverse_paired.fq --pe1-89 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M35/Sample_M35.forward_paired.fq --pe2-89 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M35/Sample_M35.reverse_paired.fq --pe1-90 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M38/Sample_M38.forward_paired.fq --pe2-90 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M38/Sample_M38.reverse_paired.fq --pe1-91 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M4/Sample_M4.forward_paired.fq --pe2-91 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M4/Sample_M4.reverse_paired.fq --pe1-92 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M40/Sample_M40.forward_paired.fq --pe2-92 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M40/Sample_M40.reverse_paired.fq --pe1-93 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M41/Sample_M41.forward_paired.fq --pe2-93 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M41/Sample_M41.reverse_paired.fq --pe1-94 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M42/Sample_M42.forward_paired.fq --pe2-94 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M42/Sample_M42.reverse_paired.fq --pe1-95 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M43/Sample_M43.forward_paired.fq --pe2-95 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M43/Sample_M43.reverse_paired.fq --pe1-96 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M46/Sample_M46.forward_paired.fq --pe2-96 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M46/Sample_M46.reverse_paired.fq --pe1-97 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M48/Sample_M48.forward_paired.fq --pe2-97 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M48/Sample_M48.reverse_paired.fq --pe1-98 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M5/Sample_M5.forward_paired.fq --pe2-98 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M5/Sample_M5.reverse_paired.fq --pe1-99 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M9/Sample_M9.forward_paired.fq --pe2-99 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_A/Sample_M9/Sample_M9.reverse_paired.fq --pe1-100 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M10/Sample_M10.forward_paired.fq --pe2-100 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M10/Sample_M10.reverse_paired.fq --pe1-101 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M12/Sample_M12.forward_paired.fq --pe2-101 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M12/Sample_M12.reverse_paired.fq --pe1-102 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M13/Sample_M13.forward_paired.fq --pe2-102 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M13/Sample_M13.reverse_paired.fq --pe1-103 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M14/Sample_M14.forward_paired.fq --pe2-103 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M14/Sample_M14.reverse_paired.fq --pe1-104 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M15/Sample_M15.forward_paired.fq --pe2-104 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M15/Sample_M15.reverse_paired.fq --pe1-105 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M17/Sample_M17.forward_paired.fq --pe2-105 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M17/Sample_M17.reverse_paired.fq --pe1-106 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M18/Sample_M18.forward_paired.fq --pe2-106 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M18/Sample_M18.reverse_paired.fq --pe1-107 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M2/Sample_M2.forward_paired.fq --pe2-107 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M2/Sample_M2.reverse_paired.fq --pe1-108 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M20/Sample_M20.forward_paired.fq --pe2-108 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M20/Sample_M20.reverse_paired.fq --pe1-109 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M23/Sample_M23.forward_paired.fq --pe2-109 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M23/Sample_M23.reverse_paired.fq --pe1-110 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M24/Sample_M24.forward_paired.fq --pe2-110 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M24/Sample_M24.reverse_paired.fq --pe1-111 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M25/Sample_M25.forward_paired.fq --pe2-111 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M25/Sample_M25.reverse_paired.fq --pe1-112 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M26/Sample_M26.forward_paired.fq --pe2-112 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M26/Sample_M26.reverse_paired.fq --pe1-113 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M27/Sample_M27.forward_paired.fq --pe2-113 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M27/Sample_M27.reverse_paired.fq --pe1-114 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M28/Sample_M28.forward_paired.fq --pe2-114 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M28/Sample_M28.reverse_paired.fq --pe1-115 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M29/Sample_M29.forward_paired.fq --pe2-115 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M29/Sample_M29.reverse_paired.fq --pe1-116 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M3/Sample_M3.forward_paired.fq --pe2-116 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M3/Sample_M3.reverse_paired.fq --pe1-117 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M30/Sample_M30.forward_paired.fq --pe2-117 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M30/Sample_M30.reverse_paired.fq --pe1-118 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M31/Sample_M31.forward_paired.fq --pe2-118 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M31/Sample_M31.reverse_paired.fq --pe1-119 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M32/Sample_M32.forward_paired.fq --pe2-119 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M32/Sample_M32.reverse_paired.fq --pe1-120 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M33/Sample_M33.forward_paired.fq --pe2-120 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M33/Sample_M33.reverse_paired.fq --pe1-121 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M34/Sample_M34.forward_paired.fq --pe2-121 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M34/Sample_M34.reverse_paired.fq --pe1-122 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M35/Sample_M35.forward_paired.fq --pe2-122 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M35/Sample_M35.reverse_paired.fq --pe1-123 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M38/Sample_M38.forward_paired.fq --pe2-123 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M38/Sample_M38.reverse_paired.fq --pe1-124 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M4/Sample_M4.forward_paired.fq --pe2-124 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M4/Sample_M4.reverse_paired.fq --pe1-125 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M40/Sample_M40.forward_paired.fq --pe2-125 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M40/Sample_M40.reverse_paired.fq --pe1-126 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M41/Sample_M41.forward_paired.fq --pe2-126 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M41/Sample_M41.reverse_paired.fq --pe1-127 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M42/Sample_M42.forward_paired.fq --pe2-127 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M42/Sample_M42.reverse_paired.fq --pe1-128 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M43/Sample_M43.forward_paired.fq --pe2-128 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M43/Sample_M43.reverse_paired.fq --pe1-129 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M46/Sample_M46.forward_paired.fq --pe2-129 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M46/Sample_M46.reverse_paired.fq --pe1-130 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M48/Sample_M48.forward_paired.fq --pe2-130 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M48/Sample_M48.reverse_paired.fq --pe1-131 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M5/Sample_M5.forward_paired.fq --pe2-131 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M5/Sample_M5.reverse_paired.fq --pe1-132 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M9/Sample_M9.forward_paired.fq --pe2-132 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150206_B/Sample_M9/Sample_M9.reverse_paired.fq --pe1-133 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M10/Sample_M10.forward_paired.fq --pe2-133 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M10/Sample_M10.reverse_paired.fq --pe1-134 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M12/Sample_M12.forward_paired.fq --pe2-134 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M12/Sample_M12.reverse_paired.fq --pe1-135 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M13/Sample_M13.forward_paired.fq --pe2-135 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M13/Sample_M13.reverse_paired.fq --pe1-136 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M14/Sample_M14.forward_paired.fq --pe2-136 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M14/Sample_M14.reverse_paired.fq --pe1-137 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M15/Sample_M15.forward_paired.fq --pe2-137 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M15/Sample_M15.reverse_paired.fq --pe1-138 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M18/Sample_M18.forward_paired.fq --pe2-138 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M18/Sample_M18.reverse_paired.fq --pe1-139 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M2/Sample_M2.forward_paired.fq --pe2-139 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M2/Sample_M2.reverse_paired.fq --pe1-140 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M20/Sample_M20.forward_paired.fq --pe2-140 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M20/Sample_M20.reverse_paired.fq --pe1-141 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M23/Sample_M23.forward_paired.fq --pe2-141 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M23/Sample_M23.reverse_paired.fq --pe1-142 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M24/Sample_M24.forward_paired.fq --pe2-142 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M24/Sample_M24.reverse_paired.fq --pe1-143 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M26/Sample_M26.forward_paired.fq --pe2-143 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M26/Sample_M26.reverse_paired.fq --pe1-144 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M27/Sample_M27.forward_paired.fq --pe2-144 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M27/Sample_M27.reverse_paired.fq --pe1-145 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M28/Sample_M28.forward_paired.fq --pe2-145 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M28/Sample_M28.reverse_paired.fq --pe1-146 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M29/Sample_M29.forward_paired.fq --pe2-146 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M29/Sample_M29.reverse_paired.fq --pe1-147 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M3/Sample_M3.forward_paired.fq --pe2-147 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M3/Sample_M3.reverse_paired.fq --pe1-148 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M31/Sample_M31.forward_paired.fq --pe2-148 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M31/Sample_M31.reverse_paired.fq --pe1-149 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M32/Sample_M32.forward_paired.fq --pe2-149 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M32/Sample_M32.reverse_paired.fq --pe1-150 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M33/Sample_M33.forward_paired.fq --pe2-150 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M33/Sample_M33.reverse_paired.fq --pe1-151 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M34/Sample_M34.forward_paired.fq --pe2-151 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M34/Sample_M34.reverse_paired.fq --pe1-152 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M35/Sample_M35.forward_paired.fq --pe2-152 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M35/Sample_M35.reverse_paired.fq --pe1-153 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M4/Sample_M4.forward_paired.fq --pe2-153 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M4/Sample_M4.reverse_paired.fq --pe1-154 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M40/Sample_M40.forward_paired.fq --pe2-154 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M40/Sample_M40.reverse_paired.fq --pe1-155 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M42/Sample_M42.forward_paired.fq --pe2-155 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M42/Sample_M42.reverse_paired.fq --pe1-156 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M43/Sample_M43.forward_paired.fq --pe2-156 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M43/Sample_M43.reverse_paired.fq --pe1-157 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M46/Sample_M46.forward_paired.fq --pe2-157 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M46/Sample_M46.reverse_paired.fq --pe1-158 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M48/Sample_M48.forward_paired.fq --pe2-158 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M48/Sample_M48.reverse_paired.fq --pe1-159 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M5/Sample_M5.forward_paired.fq --pe2-159 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M5/Sample_M5.reverse_paired.fq --pe1-160 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M9/Sample_M9.forward_paired.fq --pe2-160 /N/dc2/projects/MicroEukMA/Paramecium/biaurelia/150226/Sample_M9/Sample_M9.reverse_paired.fq -t 16 -o SPAdes-3.5.0-biaurelia-MA-only