[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2075956 sequences (280000238 bp)...
[M::process] 2075956 single-end sequences; 0 paired-end sequences
[M::process] read 2018108 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2075956 reads in 969.088 CPU sec, 44.212 real sec
[M::process] 2018108 single-end sequences; 0 paired-end sequences
[M::process] read 2040918 sequences (280000127 bp)...
[M::mem_process_seqs] Processed 2018108 reads in 975.113 CPU sec, 34.960 real sec
[M::process] 2040918 single-end sequences; 0 paired-end sequences
[M::process] read 2041520 sequences (280000094 bp)...
[M::mem_process_seqs] Processed 2040918 reads in 970.552 CPU sec, 34.824 real sec
[M::process] 2041520 single-end sequences; 0 paired-end sequences
[M::process] read 2025124 sequences (280000277 bp)...
[M::mem_process_seqs] Processed 2041520 reads in 974.066 CPU sec, 34.928 real sec
[M::process] 2025124 single-end sequences; 0 paired-end sequences
[M::process] read 2039778 sequences (280000021 bp)...
[M::mem_process_seqs] Processed 2025124 reads in 979.907 CPU sec, 35.131 real sec
[M::process] 2039778 single-end sequences; 0 paired-end sequences
[M::process] read 2068436 sequences (280000132 bp)...
[M::mem_process_seqs] Processed 2039778 reads in 978.213 CPU sec, 35.104 real sec
[M::process] 2068436 single-end sequences; 0 paired-end sequences
[M::process] read 2147936 sequences (280000233 bp)...
[M::mem_process_seqs] Processed 2068436 reads in 974.692 CPU sec, 35.169 real sec
[M::process] 2147936 single-end sequences; 0 paired-end sequences
[M::process] read 2063554 sequences (280000096 bp)...
[M::mem_process_seqs] Processed 2147936 reads in 973.433 CPU sec, 34.914 real sec
[M::process] 2063554 single-end sequences; 0 paired-end sequences
[M::process] read 2024092 sequences (280000115 bp)...
[M::mem_process_seqs] Processed 2063554 reads in 978.812 CPU sec, 35.131 real sec
[M::process] 2024092 single-end sequences; 0 paired-end sequences
[M::process] read 2049420 sequences (280000284 bp)...
[M::mem_process_seqs] Processed 2024092 reads in 977.476 CPU sec, 35.039 real sec
[M::process] 2049420 single-end sequences; 0 paired-end sequences
[M::process] read 2036068 sequences (280000061 bp)...
[M::mem_process_seqs] Processed 2049420 reads in 1004.228 CPU sec, 51.194 real sec
[M::process] 2036068 single-end sequences; 0 paired-end sequences
[M::process] read 2070096 sequences (280000279 bp)...
[M::mem_process_seqs] Processed 2036068 reads in 982.854 CPU sec, 35.224 real sec
[M::process] 2070096 single-end sequences; 0 paired-end sequences
[M::process] read 2024794 sequences (280000090 bp)...
[M::mem_process_seqs] Processed 2070096 reads in 978.455 CPU sec, 35.100 real sec
[M::process] 2024794 single-end sequences; 0 paired-end sequences
[M::process] read 2027424 sequences (280000112 bp)...
[M::mem_process_seqs] Processed 2024794 reads in 981.807 CPU sec, 35.231 real sec
[M::process] 2027424 single-end sequences; 0 paired-end sequences
[M::process] read 2080706 sequences (280000055 bp)...
[M::mem_process_seqs] Processed 2027424 reads in 981.560 CPU sec, 35.401 real sec
[M::process] 2080706 single-end sequences; 0 paired-end sequences
[M::process] read 2054892 sequences (280000085 bp)...
[M::mem_process_seqs] Processed 2080706 reads in 982.804 CPU sec, 35.217 real sec
[M::process] 2054892 single-end sequences; 0 paired-end sequences
[M::process] read 2001230 sequences (280000053 bp)...
[M::mem_process_seqs] Processed 2054892 reads in 984.956 CPU sec, 35.332 real sec
[M::process] 2001230 single-end sequences; 0 paired-end sequences
[M::process] read 2029090 sequences (280000185 bp)...
[M::mem_process_seqs] Processed 2001230 reads in 980.332 CPU sec, 35.139 real sec
[M::process] 2029090 single-end sequences; 0 paired-end sequences
[M::process] read 2037860 sequences (280000078 bp)...
[M::mem_process_seqs] Processed 2029090 reads in 1000.016 CPU sec, 45.128 real sec
[M::process] 2037860 single-end sequences; 0 paired-end sequences
[M::process] read 2074838 sequences (280000051 bp)...
[M::mem_process_seqs] Processed 2037860 reads in 985.006 CPU sec, 35.315 real sec
[M::process] 2074838 single-end sequences; 0 paired-end sequences
[M::process] read 1993786 sequences (280000091 bp)...
[M::mem_process_seqs] Processed 2074838 reads in 991.272 CPU sec, 35.534 real sec
[M::process] 1993786 single-end sequences; 0 paired-end sequences
[M::process] read 2020308 sequences (280000079 bp)...
[M::mem_process_seqs] Processed 1993786 reads in 994.243 CPU sec, 35.633 real sec
[M::process] 2020308 single-end sequences; 0 paired-end sequences
[M::process] read 2029290 sequences (280000186 bp)...
[M::mem_process_seqs] Processed 2020308 reads in 994.458 CPU sec, 40.008 real sec
[M::process] 2029290 single-end sequences; 0 paired-end sequences
[M::process] read 2081916 sequences (280000089 bp)...
[M::mem_process_seqs] Processed 2029290 reads in 984.748 CPU sec, 35.309 real sec
[M::process] 2081916 single-end sequences; 0 paired-end sequences
[M::process] read 2049968 sequences (280000111 bp)...
[M::mem_process_seqs] Processed 2081916 reads in 991.636 CPU sec, 35.583 real sec
[M::process] 2049968 single-end sequences; 0 paired-end sequences
[M::process] read 2025234 sequences (280000117 bp)...
[M::mem_process_seqs] Processed 2049968 reads in 997.199 CPU sec, 35.754 real sec
[M::process] 2025234 single-end sequences; 0 paired-end sequences
[M::process] read 2064154 sequences (280000249 bp)...
[M::mem_process_seqs] Processed 2025234 reads in 991.477 CPU sec, 35.568 real sec
[M::process] 2064154 single-end sequences; 0 paired-end sequences
[M::process] read 2102474 sequences (280000171 bp)...
[M::mem_process_seqs] Processed 2064154 reads in 982.886 CPU sec, 35.255 real sec
[M::process] 2102474 single-end sequences; 0 paired-end sequences
[M::process] read 2034072 sequences (280000167 bp)...
[M::mem_process_seqs] Processed 2102474 reads in 975.491 CPU sec, 34.975 real sec
[M::process] 2034072 single-end sequences; 0 paired-end sequences
[M::process] read 2020960 sequences (280000031 bp)...
[M::mem_process_seqs] Processed 2034072 reads in 975.741 CPU sec, 34.992 real sec
[M::process] 2020960 single-end sequences; 0 paired-end sequences
[M::process] read 2036750 sequences (280000052 bp)...
[M::mem_process_seqs] Processed 2020960 reads in 973.162 CPU sec, 35.627 real sec
[M::process] 2036750 single-end sequences; 0 paired-end sequences
[M::process] read 2027376 sequences (280000060 bp)...
[M::mem_process_seqs] Processed 2036750 reads in 976.483 CPU sec, 35.009 real sec
[M::process] 2027376 single-end sequences; 0 paired-end sequences
[M::process] read 2037548 sequences (280000062 bp)...
[M::mem_process_seqs] Processed 2027376 reads in 978.851 CPU sec, 35.135 real sec
[M::process] 2037548 single-end sequences; 0 paired-end sequences
[M::process] read 2050902 sequences (280000228 bp)...
[M::mem_process_seqs] Processed 2037548 reads in 980.954 CPU sec, 35.208 real sec
[M::process] 2050902 single-end sequences; 0 paired-end sequences
[M::process] read 2109670 sequences (280000216 bp)...
[M::mem_process_seqs] Processed 2050902 reads in 977.013 CPU sec, 38.128 real sec
[M::process] 2109670 single-end sequences; 0 paired-end sequences
[M::process] read 2064994 sequences (280000069 bp)...
[M::mem_process_seqs] Processed 2109670 reads in 984.457 CPU sec, 35.316 real sec
[M::process] 2064994 single-end sequences; 0 paired-end sequences
[M::process] read 2064064 sequences (280000299 bp)...
[M::mem_process_seqs] Processed 2064994 reads in 977.640 CPU sec, 35.061 real sec
[M::process] 2064064 single-end sequences; 0 paired-end sequences
[M::process] read 2014166 sequences (280000007 bp)...
[M::mem_process_seqs] Processed 2064064 reads in 981.167 CPU sec, 35.225 real sec
[M::process] 2014166 single-end sequences; 0 paired-end sequences
[M::process] read 2044464 sequences (280000034 bp)...
[M::mem_process_seqs] Processed 2014166 reads in 984.315 CPU sec, 36.282 real sec
[M::process] 2044464 single-end sequences; 0 paired-end sequences
[M::process] read 2056992 sequences (280000153 bp)...
[M::mem_process_seqs] Processed 2044464 reads in 984.268 CPU sec, 35.290 real sec
[M::process] 2056992 single-end sequences; 0 paired-end sequences
[M::process] read 2024108 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2056992 reads in 978.954 CPU sec, 35.086 real sec
[M::process] 2024108 single-end sequences; 0 paired-end sequences
[M::process] read 2093418 sequences (280000044 bp)...
[M::mem_process_seqs] Processed 2024108 reads in 983.245 CPU sec, 35.247 real sec
[M::process] 2093418 single-end sequences; 0 paired-end sequences
[M::process] read 2058530 sequences (280000069 bp)...
[M::mem_process_seqs] Processed 2093418 reads in 999.327 CPU sec, 43.201 real sec
[M::process] 2058530 single-end sequences; 0 paired-end sequences
[M::process] read 2042192 sequences (280000041 bp)...
[M::mem_process_seqs] Processed 2058530 reads in 987.468 CPU sec, 35.400 real sec
[M::process] 2042192 single-end sequences; 0 paired-end sequences
[M::process] read 2005286 sequences (280000216 bp)...
[M::mem_process_seqs] Processed 2042192 reads in 982.666 CPU sec, 35.246 real sec
[M::process] 2005286 single-end sequences; 0 paired-end sequences
[M::process] read 2030566 sequences (280000280 bp)...
[M::mem_process_seqs] Processed 2005286 reads in 987.900 CPU sec, 35.394 real sec
[M::process] 2030566 single-end sequences; 0 paired-end sequences
[M::process] read 2040712 sequences (280000282 bp)...
[M::mem_process_seqs] Processed 2030566 reads in 992.486 CPU sec, 36.528 real sec
[M::process] 2040712 single-end sequences; 0 paired-end sequences
[M::process] read 2048544 sequences (280000118 bp)...
[M::mem_process_seqs] Processed 2040712 reads in 982.295 CPU sec, 35.212 real sec
[M::process] 2048544 single-end sequences; 0 paired-end sequences
[M::process] read 2028870 sequences (280000193 bp)...
[M::mem_process_seqs] Processed 2048544 reads in 989.752 CPU sec, 35.478 real sec
[M::process] 2028870 single-end sequences; 0 paired-end sequences
[M::process] read 2002272 sequences (280000020 bp)...
[M::mem_process_seqs] Processed 2028870 reads in 986.298 CPU sec, 35.405 real sec
[M::process] 2002272 single-end sequences; 0 paired-end sequences
[M::process] read 2042524 sequences (280000062 bp)...
[M::mem_process_seqs] Processed 2002272 reads in 999.244 CPU sec, 42.341 real sec
[M::process] 2042524 single-end sequences; 0 paired-end sequences
[M::process] read 2121978 sequences (280000252 bp)...
[M::mem_process_seqs] Processed 2042524 reads in 993.788 CPU sec, 35.627 real sec
[M::process] 2121978 single-end sequences; 0 paired-end sequences
[M::process] read 2032622 sequences (280000058 bp)...
[M::mem_process_seqs] Processed 2121978 reads in 991.339 CPU sec, 35.570 real sec
[M::process] 2032622 single-end sequences; 0 paired-end sequences
[M::process] read 2029192 sequences (280000084 bp)...
[M::mem_process_seqs] Processed 2032622 reads in 996.879 CPU sec, 35.764 real sec
[M::process] 2029192 single-end sequences; 0 paired-end sequences
[M::process] read 2090842 sequences (280000245 bp)...
[M::mem_process_seqs] Processed 2029192 reads in 993.538 CPU sec, 36.531 real sec
[M::process] 2090842 single-end sequences; 0 paired-end sequences
[M::process] read 2110816 sequences (280000134 bp)...
[M::mem_process_seqs] Processed 2090842 reads in 981.771 CPU sec, 35.241 real sec
[M::process] 2110816 single-end sequences; 0 paired-end sequences
[M::process] read 2023216 sequences (280000188 bp)...
[M::mem_process_seqs] Processed 2110816 reads in 974.344 CPU sec, 34.941 real sec
[M::process] 2023216 single-end sequences; 0 paired-end sequences
[M::process] read 2023894 sequences (280000172 bp)...
[M::mem_process_seqs] Processed 2023216 reads in 979.288 CPU sec, 35.114 real sec
[M::process] 2023894 single-end sequences; 0 paired-end sequences
[M::process] read 2010334 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2023894 reads in 1010.957 CPU sec, 50.317 real sec
[M::process] 2010334 single-end sequences; 0 paired-end sequences
[M::process] read 2013220 sequences (280000291 bp)...
[M::mem_process_seqs] Processed 2010334 reads in 981.363 CPU sec, 35.193 real sec
[M::process] 2013220 single-end sequences; 0 paired-end sequences
[M::process] read 2025132 sequences (280000237 bp)...
[M::mem_process_seqs] Processed 2013220 reads in 981.638 CPU sec, 35.239 real sec
[M::process] 2025132 single-end sequences; 0 paired-end sequences
[M::process] read 2082884 sequences (280000097 bp)...
[M::mem_process_seqs] Processed 2025132 reads in 988.596 CPU sec, 35.450 real sec
[M::process] 2082884 single-end sequences; 0 paired-end sequences
[M::process] read 2103620 sequences (280000025 bp)...
[M::mem_process_seqs] Processed 2082884 reads in 1017.934 CPU sec, 36.698 real sec
[M::process] 2103620 single-end sequences; 0 paired-end sequences
[M::process] read 2049078 sequences (280000300 bp)...
[M::mem_process_seqs] Processed 2103620 reads in 994.873 CPU sec, 35.686 real sec
[M::process] 2049078 single-end sequences; 0 paired-end sequences
[M::process] read 2053024 sequences (280000256 bp)...
[M::mem_process_seqs] Processed 2049078 reads in 1001.402 CPU sec, 35.903 real sec
[M::process] 2053024 single-end sequences; 0 paired-end sequences
[M::process] read 2035726 sequences (280000098 bp)...
[M::mem_process_seqs] Processed 2053024 reads in 986.799 CPU sec, 35.408 real sec
[M::process] 2035726 single-end sequences; 0 paired-end sequences
[M::process] read 2066670 sequences (280000226 bp)...
[M::mem_process_seqs] Processed 2035726 reads in 1017.458 CPU sec, 37.070 real sec
[M::process] 2066670 single-end sequences; 0 paired-end sequences
[M::process] read 2063170 sequences (280000194 bp)...
[M::mem_process_seqs] Processed 2066670 reads in 1021.790 CPU sec, 36.681 real sec
[M::process] 2063170 single-end sequences; 0 paired-end sequences
[M::process] read 2027754 sequences (280000214 bp)...
[M::mem_process_seqs] Processed 2063170 reads in 1019.961 CPU sec, 36.567 real sec
[M::process] 2027754 single-end sequences; 0 paired-end sequences
[M::process] read 2080566 sequences (280000228 bp)...
[M::mem_process_seqs] Processed 2027754 reads in 1005.997 CPU sec, 36.061 real sec
[M::process] 2080566 single-end sequences; 0 paired-end sequences
[M::process] read 2050688 sequences (280000064 bp)...
[M::mem_process_seqs] Processed 2080566 reads in 1007.136 CPU sec, 47.988 real sec
[M::process] 2050688 single-end sequences; 0 paired-end sequences
[M::process] read 2051852 sequences (280000134 bp)...
[M::mem_process_seqs] Processed 2050688 reads in 982.858 CPU sec, 35.251 real sec
[M::process] 2051852 single-end sequences; 0 paired-end sequences
[M::process] read 2015830 sequences (280000200 bp)...
[M::mem_process_seqs] Processed 2051852 reads in 986.092 CPU sec, 35.365 real sec
[M::process] 2015830 single-end sequences; 0 paired-end sequences
[M::process] read 2017756 sequences (280000017 bp)...
[M::mem_process_seqs] Processed 2015830 reads in 984.186 CPU sec, 35.273 real sec
[M::process] 2017756 single-end sequences; 0 paired-end sequences
[M::process] read 2050064 sequences (280000028 bp)...
[M::mem_process_seqs] Processed 2017756 reads in 1005.400 CPU sec, 36.907 real sec
[M::process] 2050064 single-end sequences; 0 paired-end sequences
[M::process] read 2045848 sequences (280000061 bp)...
[M::mem_process_seqs] Processed 2050064 reads in 1026.170 CPU sec, 36.840 real sec
[M::process] 2045848 single-end sequences; 0 paired-end sequences
[M::process] read 2020892 sequences (280000202 bp)...
[M::mem_process_seqs] Processed 2045848 reads in 1011.949 CPU sec, 36.268 real sec
[M::process] 2020892 single-end sequences; 0 paired-end sequences
[M::process] read 2046854 sequences (280000078 bp)...
[M::mem_process_seqs] Processed 2020892 reads in 998.480 CPU sec, 35.792 real sec
[M::process] 2046854 single-end sequences; 0 paired-end sequences
[M::process] read 2114224 sequences (280000045 bp)...
[M::mem_process_seqs] Processed 2046854 reads in 1039.665 CPU sec, 45.227 real sec
[M::process] 2114224 single-end sequences; 0 paired-end sequences
[M::process] read 2112080 sequences (280000058 bp)...
[M::mem_process_seqs] Processed 2114224 reads in 1022.637 CPU sec, 36.656 real sec
[M::process] 2112080 single-end sequences; 0 paired-end sequences
[M::process] read 2017194 sequences (280000261 bp)...
[M::mem_process_seqs] Processed 2112080 reads in 1008.396 CPU sec, 36.187 real sec
[M::process] 2017194 single-end sequences; 0 paired-end sequences
[M::process] read 2024156 sequences (280000290 bp)...
[M::mem_process_seqs] Processed 2017194 reads in 985.769 CPU sec, 35.323 real sec
[M::process] 2024156 single-end sequences; 0 paired-end sequences
[M::process] read 2083896 sequences (280000070 bp)...
[M::mem_process_seqs] Processed 2024156 reads in 990.224 CPU sec, 37.504 real sec
[M::process] 2083896 single-end sequences; 0 paired-end sequences
[M::process] read 2044370 sequences (280000027 bp)...
[M::mem_process_seqs] Processed 2083896 reads in 964.423 CPU sec, 34.610 real sec
[M::process] 2044370 single-end sequences; 0 paired-end sequences
[M::process] read 2034952 sequences (280000117 bp)...
[M::mem_process_seqs] Processed 2044370 reads in 971.265 CPU sec, 34.849 real sec
[M::process] 2034952 single-end sequences; 0 paired-end sequences
[M::process] read 2043554 sequences (280000200 bp)...
[M::mem_process_seqs] Processed 2034952 reads in 966.493 CPU sec, 34.675 real sec
[M::process] 2043554 single-end sequences; 0 paired-end sequences
[M::process] read 2019586 sequences (280000271 bp)...
[M::mem_process_seqs] Processed 2043554 reads in 970.964 CPU sec, 34.901 real sec
[M::process] 2019586 single-end sequences; 0 paired-end sequences
[M::process] read 2018106 sequences (280000057 bp)...
[M::mem_process_seqs] Processed 2019586 reads in 980.194 CPU sec, 35.134 real sec
[M::process] 2018106 single-end sequences; 0 paired-end sequences
[M::process] read 2019640 sequences (280000180 bp)...
[M::mem_process_seqs] Processed 2018106 reads in 976.151 CPU sec, 34.992 real sec
[M::process] 2019640 single-end sequences; 0 paired-end sequences
[M::process] read 2113622 sequences (280000054 bp)...
[M::mem_process_seqs] Processed 2019640 reads in 974.788 CPU sec, 34.986 real sec
[M::process] 2113622 single-end sequences; 0 paired-end sequences
[M::process] read 2037512 sequences (280000078 bp)...
[M::mem_process_seqs] Processed 2113622 reads in 965.055 CPU sec, 34.618 real sec
[M::process] 2037512 single-end sequences; 0 paired-end sequences
[M::process] read 2039710 sequences (280000252 bp)...
[M::mem_process_seqs] Processed 2037512 reads in 972.270 CPU sec, 34.848 real sec
[M::process] 2039710 single-end sequences; 0 paired-end sequences
[M::process] read 2050924 sequences (280000016 bp)...
[M::mem_process_seqs] Processed 2039710 reads in 974.949 CPU sec, 34.961 real sec
[M::process] 2050924 single-end sequences; 0 paired-end sequences
[M::process] read 2022160 sequences (280000017 bp)...
[M::mem_process_seqs] Processed 2050924 reads in 970.426 CPU sec, 34.769 real sec
[M::process] 2022160 single-end sequences; 0 paired-end sequences
[M::process] read 2034180 sequences (280000184 bp)...
[M::mem_process_seqs] Processed 2022160 reads in 969.313 CPU sec, 34.769 real sec
[M::process] 2034180 single-end sequences; 0 paired-end sequences
[M::process] read 2001292 sequences (280000029 bp)...
[M::mem_process_seqs] Processed 2034180 reads in 969.492 CPU sec, 34.762 real sec
[M::process] 2001292 single-end sequences; 0 paired-end sequences
[M::process] read 2046974 sequences (280000037 bp)...
[M::mem_process_seqs] Processed 2001292 reads in 977.385 CPU sec, 39.710 real sec
[M::process] 2046974 single-end sequences; 0 paired-end sequences
[M::process] read 2088650 sequences (280000244 bp)...
[M::mem_process_seqs] Processed 2046974 reads in 984.074 CPU sec, 35.255 real sec
[M::process] 2088650 single-end sequences; 0 paired-end sequences
[M::process] read 2040888 sequences (280000036 bp)...
[M::mem_process_seqs] Processed 2088650 reads in 984.384 CPU sec, 35.320 real sec
[M::process] 2040888 single-end sequences; 0 paired-end sequences
[M::process] read 2047570 sequences (280000248 bp)...
[M::mem_process_seqs] Processed 2040888 reads in 993.361 CPU sec, 35.635 real sec
[M::process] 2047570 single-end sequences; 0 paired-end sequences
[M::process] read 2046272 sequences (280000270 bp)...
[M::mem_process_seqs] Processed 2047570 reads in 1015.842 CPU sec, 36.406 real sec
[M::process] 2046272 single-end sequences; 0 paired-end sequences
[M::process] read 2048706 sequences (280000267 bp)...
[M::mem_process_seqs] Processed 2046272 reads in 995.454 CPU sec, 35.682 real sec
[M::process] 2048706 single-end sequences; 0 paired-end sequences
[M::process] read 2071652 sequences (280000235 bp)...
[M::mem_process_seqs] Processed 2048706 reads in 980.066 CPU sec, 35.140 real sec
[M::process] 2071652 single-end sequences; 0 paired-end sequences
[M::process] read 2011196 sequences (280000153 bp)...
[M::mem_process_seqs] Processed 2071652 reads in 972.795 CPU sec, 34.855 real sec
[M::process] 2011196 single-end sequences; 0 paired-end sequences
[M::process] read 2026746 sequences (280000050 bp)...
[M::mem_process_seqs] Processed 2011196 reads in 977.183 CPU sec, 35.018 real sec
[M::process] 2026746 single-end sequences; 0 paired-end sequences
[M::process] read 2040738 sequences (280000027 bp)...
[M::mem_process_seqs] Processed 2026746 reads in 983.476 CPU sec, 35.273 real sec
[M::process] 2040738 single-end sequences; 0 paired-end sequences
[M::process] read 2094804 sequences (280000120 bp)...
[M::mem_process_seqs] Processed 2040738 reads in 986.294 CPU sec, 42.055 real sec
[M::process] 2094804 single-end sequences; 0 paired-end sequences
[M::process] read 2045394 sequences (280000075 bp)...
[M::mem_process_seqs] Processed 2094804 reads in 976.139 CPU sec, 35.009 real sec
[M::process] 2045394 single-end sequences; 0 paired-end sequences
[M::process] read 2038094 sequences (280000221 bp)...
[M::mem_process_seqs] Processed 2045394 reads in 981.341 CPU sec, 35.170 real sec
[M::process] 2038094 single-end sequences; 0 paired-end sequences
[M::process] read 1409090 sequences (187814398 bp)...
[M::mem_process_seqs] Processed 2038094 reads in 979.219 CPU sec, 35.133 real sec
[M::process] 1409090 single-end sequences; 0 paired-end sequences
[M::mem_process_seqs] Processed 1409090 reads in 656.836 CPU sec, 23.844 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /gscratch/srlab/programs/bwa-0.7.15/bwa mem -t 28 -R @RG\tID:Pcod1\tSM:WA\tPL:illumina\tLB:lib1\tPU:unit1 -p ./atl_cod_4_2017 ACAGCTGT_6.1_trimmed.fastq
[main] Real time: 4059.792 sec; CPU: 109278.615 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2429758 sequences (280000236 bp)...
[M::process] 2429758 single-end sequences; 0 paired-end sequences
[M::process] read 2325094 sequences (280000243 bp)...
[M::mem_process_seqs] Processed 2429758 reads in 937.472 CPU sec, 47.883 real sec
[M::process] 2325094 single-end sequences; 0 paired-end sequences
[M::process] read 2338654 sequences (280000210 bp)...
[M::mem_process_seqs] Processed 2325094 reads in 938.241 CPU sec, 33.685 real sec
[M::process] 2338654 single-end sequences; 0 paired-end sequences
[M::process] read 2241442 sequences (280000137 bp)...
[M::mem_process_seqs] Processed 2338654 reads in 938.410 CPU sec, 33.650 real sec
[M::process] 2241442 single-end sequences; 0 paired-end sequences
[M::process] read 2249994 sequences (280000028 bp)...
[M::mem_process_seqs] Processed 2241442 reads in 941.987 CPU sec, 33.830 real sec
[M::process] 2249994 single-end sequences; 0 paired-end sequences
[M::process] read 2371314 sequences (280000085 bp)...
[M::mem_process_seqs] Processed 2249994 reads in 950.752 CPU sec, 36.532 real sec
[M::process] 2371314 single-end sequences; 0 paired-end sequences
[M::process] read 2349640 sequences (280000069 bp)...
[M::mem_process_seqs] Processed 2371314 reads in 949.470 CPU sec, 34.059 real sec
[M::process] 2349640 single-end sequences; 0 paired-end sequences
[M::process] read 2338760 sequences (280000021 bp)...
[M::mem_process_seqs] Processed 2349640 reads in 957.163 CPU sec, 34.326 real sec
[M::process] 2338760 single-end sequences; 0 paired-end sequences
[M::process] read 2358758 sequences (280000025 bp)...
[M::mem_process_seqs] Processed 2338760 reads in 950.601 CPU sec, 34.095 real sec
[M::process] 2358758 single-end sequences; 0 paired-end sequences
[M::process] read 2277394 sequences (280000129 bp)...
[M::mem_process_seqs] Processed 2358758 reads in 955.243 CPU sec, 34.266 real sec
[M::process] 2277394 single-end sequences; 0 paired-end sequences
[M::process] read 2316230 sequences (280000146 bp)...
[M::mem_process_seqs] Processed 2277394 reads in 949.822 CPU sec, 34.145 real sec
[M::process] 2316230 single-end sequences; 0 paired-end sequences
[M::process] read 2282364 sequences (280000171 bp)...
[M::mem_process_seqs] Processed 2316230 reads in 950.071 CPU sec, 34.058 real sec
[M::process] 2282364 single-end sequences; 0 paired-end sequences
[M::process] read 2357224 sequences (280000150 bp)...
[M::mem_process_seqs] Processed 2282364 reads in 945.813 CPU sec, 33.913 real sec
[M::process] 2357224 single-end sequences; 0 paired-end sequences
[M::process] read 2308974 sequences (280000108 bp)...
[M::mem_process_seqs] Processed 2357224 reads in 969.773 CPU sec, 45.824 real sec
[M::process] 2308974 single-end sequences; 0 paired-end sequences
[M::process] read 2293472 sequences (280000211 bp)...
[M::mem_process_seqs] Processed 2308974 reads in 952.469 CPU sec, 34.192 real sec
[M::process] 2293472 single-end sequences; 0 paired-end sequences
[M::process] read 2279716 sequences (280000006 bp)...
[M::mem_process_seqs] Processed 2293472 reads in 953.630 CPU sec, 34.213 real sec
[M::process] 2279716 single-end sequences; 0 paired-end sequences
[M::process] read 2331660 sequences (280000042 bp)...
[M::mem_process_seqs] Processed 2279716 reads in 963.560 CPU sec, 34.572 real sec
[M::process] 2331660 single-end sequences; 0 paired-end sequences
[M::process] read 2304042 sequences (280000206 bp)...
[M::mem_process_seqs] Processed 2331660 reads in 962.197 CPU sec, 38.283 real sec
[M::process] 2304042 single-end sequences; 0 paired-end sequences
[M::process] read 2270352 sequences (280000260 bp)...
[M::mem_process_seqs] Processed 2304042 reads in 954.266 CPU sec, 34.256 real sec
[M::process] 2270352 single-end sequences; 0 paired-end sequences
[M::process] read 2333810 sequences (280000022 bp)...
[M::mem_process_seqs] Processed 2270352 reads in 962.862 CPU sec, 34.543 real sec
[M::process] 2333810 single-end sequences; 0 paired-end sequences
[M::process] read 2425636 sequences (280000076 bp)...
[M::mem_process_seqs] Processed 2333810 reads in 957.340 CPU sec, 34.395 real sec
[M::process] 2425636 single-end sequences; 0 paired-end sequences
[M::process] read 2303754 sequences (280000030 bp)...
[M::mem_process_seqs] Processed 2425636 reads in 962.191 CPU sec, 34.533 real sec
[M::process] 2303754 single-end sequences; 0 paired-end sequences
[M::process] read 2338748 sequences (280000018 bp)...
[M::mem_process_seqs] Processed 2303754 reads in 960.113 CPU sec, 34.457 real sec
[M::process] 2338748 single-end sequences; 0 paired-end sequences
[M::process] read 2391602 sequences (280000020 bp)...
[M::mem_process_seqs] Processed 2338748 reads in 957.326 CPU sec, 36.338 real sec
[M::process] 2391602 single-end sequences; 0 paired-end sequences
[M::process] read 2272054 sequences (280000276 bp)...
[M::mem_process_seqs] Processed 2391602 reads in 928.458 CPU sec, 33.288 real sec
[M::process] 2272054 single-end sequences; 0 paired-end sequences
[M::process] read 2340064 sequences (280000120 bp)...
[M::mem_process_seqs] Processed 2272054 reads in 937.639 CPU sec, 33.628 real sec
[M::process] 2340064 single-end sequences; 0 paired-end sequences
[M::process] read 2245936 sequences (280000042 bp)...
[M::mem_process_seqs] Processed 2340064 reads in 939.664 CPU sec, 33.756 real sec
[M::process] 2245936 single-end sequences; 0 paired-end sequences
[M::process] read 2260232 sequences (280000157 bp)...
[M::mem_process_seqs] Processed 2245936 reads in 947.868 CPU sec, 34.008 real sec
[M::process] 2260232 single-end sequences; 0 paired-end sequences
[M::process] read 2321250 sequences (280000001 bp)...
[M::mem_process_seqs] Processed 2260232 reads in 949.195 CPU sec, 34.084 real sec
[M::process] 2321250 single-end sequences; 0 paired-end sequences
[M::process] read 2326314 sequences (280000267 bp)...
[M::mem_process_seqs] Processed 2321250 reads in 949.674 CPU sec, 34.097 real sec
[M::process] 2326314 single-end sequences; 0 paired-end sequences
[M::process] read 2305954 sequences (280000244 bp)...
[M::mem_process_seqs] Processed 2326314 reads in 956.869 CPU sec, 34.357 real sec
[M::process] 2305954 single-end sequences; 0 paired-end sequences
[M::process] read 2316716 sequences (280000056 bp)...
[M::mem_process_seqs] Processed 2305954 reads in 954.705 CPU sec, 34.237 real sec
[M::process] 2316716 single-end sequences; 0 paired-end sequences
[M::process] read 2295174 sequences (280000043 bp)...
[M::mem_process_seqs] Processed 2316716 reads in 952.789 CPU sec, 34.249 real sec
[M::process] 2295174 single-end sequences; 0 paired-end sequences
[M::process] read 2309450 sequences (280000237 bp)...
[M::mem_process_seqs] Processed 2295174 reads in 957.288 CPU sec, 36.302 real sec
[M::process] 2309450 single-end sequences; 0 paired-end sequences
[M::process] read 2291372 sequences (280000134 bp)...
[M::mem_process_seqs] Processed 2309450 reads in 951.533 CPU sec, 34.137 real sec
[M::process] 2291372 single-end sequences; 0 paired-end sequences
[M::process] read 2424334 sequences (280000030 bp)...
[M::mem_process_seqs] Processed 2291372 reads in 950.373 CPU sec, 34.150 real sec
[M::process] 2424334 single-end sequences; 0 paired-end sequences
[M::process] read 2355618 sequences (280000137 bp)...
[M::mem_process_seqs] Processed 2424334 reads in 952.613 CPU sec, 34.206 real sec
[M::process] 2355618 single-end sequences; 0 paired-end sequences
[M::process] read 2260420 sequences (280000075 bp)...
[M::mem_process_seqs] Processed 2355618 reads in 956.500 CPU sec, 34.338 real sec
[M::process] 2260420 single-end sequences; 0 paired-end sequences
[M::process] read 2296618 sequences (280000104 bp)...
[M::mem_process_seqs] Processed 2260420 reads in 959.319 CPU sec, 34.414 real sec
[M::process] 2296618 single-end sequences; 0 paired-end sequences
[M::process] read 2325518 sequences (280000091 bp)...
[M::mem_process_seqs] Processed 2296618 reads in 978.961 CPU sec, 46.351 real sec
[M::process] 2325518 single-end sequences; 0 paired-end sequences
[M::process] read 2297954 sequences (280000120 bp)...
[M::mem_process_seqs] Processed 2325518 reads in 954.796 CPU sec, 34.257 real sec
[M::process] 2297954 single-end sequences; 0 paired-end sequences
[M::process] read 2291536 sequences (280000029 bp)...
[M::mem_process_seqs] Processed 2297954 reads in 962.056 CPU sec, 34.528 real sec
[M::process] 2291536 single-end sequences; 0 paired-end sequences
[M::process] read 2352402 sequences (280000019 bp)...
[M::mem_process_seqs] Processed 2291536 reads in 956.557 CPU sec, 34.364 real sec
[M::process] 2352402 single-end sequences; 0 paired-end sequences
[M::process] read 2447352 sequences (280000164 bp)...
[M::mem_process_seqs] Processed 2352402 reads in 959.925 CPU sec, 34.828 real sec
[M::process] 2447352 single-end sequences; 0 paired-end sequences
[M::process] read 2311626 sequences (280000162 bp)...
[M::mem_process_seqs] Processed 2447352 reads in 959.596 CPU sec, 34.407 real sec
[M::process] 2311626 single-end sequences; 0 paired-end sequences
[M::process] read 2421162 sequences (280000198 bp)...
[M::mem_process_seqs] Processed 2311626 reads in 961.964 CPU sec, 34.506 real sec
[M::process] 2421162 single-end sequences; 0 paired-end sequences
[M::process] read 2516002 sequences (280000168 bp)...
[M::mem_process_seqs] Processed 2421162 reads in 961.190 CPU sec, 34.507 real sec
[M::process] 2516002 single-end sequences; 0 paired-end sequences
[M::process] read 2359132 sequences (280000114 bp)...
[M::mem_process_seqs] Processed 2516002 reads in 967.063 CPU sec, 49.889 real sec
[M::process] 2359132 single-end sequences; 0 paired-end sequences
[M::process] read 2340872 sequences (280000084 bp)...
[M::mem_process_seqs] Processed 2359132 reads in 949.747 CPU sec, 34.063 real sec
[M::process] 2340872 single-end sequences; 0 paired-end sequences
[M::process] read 2296298 sequences (280000026 bp)...
[M::mem_process_seqs] Processed 2340872 reads in 946.510 CPU sec, 33.980 real sec
[M::process] 2296298 single-end sequences; 0 paired-end sequences
[M::process] read 2357312 sequences (280000097 bp)...
[M::mem_process_seqs] Processed 2296298 reads in 964.449 CPU sec, 34.647 real sec
[M::process] 2357312 single-end sequences; 0 paired-end sequences
[M::process] read 2486212 sequences (280000039 bp)...
[M::mem_process_seqs] Processed 2357312 reads in 994.663 CPU sec, 36.163 real sec
[M::process] 2486212 single-end sequences; 0 paired-end sequences
[M::process] read 2478388 sequences (280000174 bp)...
[M::mem_process_seqs] Processed 2486212 reads in 960.839 CPU sec, 34.535 real sec
[M::process] 2478388 single-end sequences; 0 paired-end sequences
[M::process] read 2441556 sequences (280000007 bp)...
[M::mem_process_seqs] Processed 2478388 reads in 988.364 CPU sec, 35.451 real sec
[M::process] 2441556 single-end sequences; 0 paired-end sequences
[M::process] read 2354678 sequences (280000179 bp)...
[M::mem_process_seqs] Processed 2441556 reads in 965.600 CPU sec, 34.679 real sec
[M::process] 2354678 single-end sequences; 0 paired-end sequences
[M::process] read 2495816 sequences (280000017 bp)...
[M::mem_process_seqs] Processed 2354678 reads in 997.473 CPU sec, 51.647 real sec
[M::process] 2495816 single-end sequences; 0 paired-end sequences
[M::process] read 2307846 sequences (280000238 bp)...
[M::mem_process_seqs] Processed 2495816 reads in 987.176 CPU sec, 35.750 real sec
[M::process] 2307846 single-end sequences; 0 paired-end sequences
[M::process] read 2396084 sequences (280000093 bp)...
[M::mem_process_seqs] Processed 2307846 reads in 964.479 CPU sec, 34.615 real sec
[M::process] 2396084 single-end sequences; 0 paired-end sequences
[M::process] read 2362374 sequences (280000204 bp)...
[M::mem_process_seqs] Processed 2396084 reads in 955.684 CPU sec, 34.302 real sec
[M::process] 2362374 single-end sequences; 0 paired-end sequences
[M::process] read 2368770 sequences (280000157 bp)...
[M::mem_process_seqs] Processed 2362374 reads in 969.522 CPU sec, 34.824 real sec
[M::process] 2368770 single-end sequences; 0 paired-end sequences
[M::process] read 2351552 sequences (280000210 bp)...
[M::mem_process_seqs] Processed 2368770 reads in 974.440 CPU sec, 35.016 real sec
[M::process] 2351552 single-end sequences; 0 paired-end sequences
[M::process] read 2452644 sequences (280000266 bp)...
[M::mem_process_seqs] Processed 2351552 reads in 983.904 CPU sec, 35.315 real sec
[M::process] 2452644 single-end sequences; 0 paired-end sequences
[M::process] read 2430512 sequences (280000126 bp)...
[M::mem_process_seqs] Processed 2452644 reads in 1020.025 CPU sec, 36.597 real sec
[M::process] 2430512 single-end sequences; 0 paired-end sequences
[M::process] read 2383882 sequences (280000239 bp)...
[M::mem_process_seqs] Processed 2430512 reads in 993.895 CPU sec, 35.679 real sec
[M::process] 2383882 single-end sequences; 0 paired-end sequences
[M::process] read 2453762 sequences (280000054 bp)...
[M::mem_process_seqs] Processed 2383882 reads in 979.180 CPU sec, 35.139 real sec
[M::process] 2453762 single-end sequences; 0 paired-end sequences
[M::process] read 2484964 sequences (280000053 bp)...
[M::mem_process_seqs] Processed 2453762 reads in 990.637 CPU sec, 37.777 real sec
[M::process] 2484964 single-end sequences; 0 paired-end sequences
[M::process] read 2370336 sequences (280000021 bp)...
[M::mem_process_seqs] Processed 2484964 reads in 969.865 CPU sec, 34.789 real sec
[M::process] 2370336 single-end sequences; 0 paired-end sequences
[M::process] read 2508856 sequences (280000167 bp)...
[M::mem_process_seqs] Processed 2370336 reads in 958.643 CPU sec, 34.419 real sec
[M::process] 2508856 single-end sequences; 0 paired-end sequences
[M::process] read 2437482 sequences (280000027 bp)...
[M::mem_process_seqs] Processed 2508856 reads in 946.772 CPU sec, 34.016 real sec
[M::process] 2437482 single-end sequences; 0 paired-end sequences
[M::process] read 2368070 sequences (280000100 bp)...
[M::mem_process_seqs] Processed 2437482 reads in 940.237 CPU sec, 33.727 real sec
[M::process] 2368070 single-end sequences; 0 paired-end sequences
[M::process] read 2339738 sequences (280000151 bp)...
[M::mem_process_seqs] Processed 2368070 reads in 937.876 CPU sec, 33.696 real sec
[M::process] 2339738 single-end sequences; 0 paired-end sequences
[M::process] read 2292888 sequences (280000008 bp)...
[M::mem_process_seqs] Processed 2339738 reads in 952.472 CPU sec, 34.181 real sec
[M::process] 2292888 single-end sequences; 0 paired-end sequences
[M::process] read 2363900 sequences (280000067 bp)...
[M::mem_process_seqs] Processed 2292888 reads in 962.843 CPU sec, 34.564 real sec
[M::process] 2363900 single-end sequences; 0 paired-end sequences
[M::process] read 2469684 sequences (280000224 bp)...
[M::mem_process_seqs] Processed 2363900 reads in 965.518 CPU sec, 34.954 real sec
[M::process] 2469684 single-end sequences; 0 paired-end sequences
[M::process] read 2315400 sequences (280000155 bp)...
[M::mem_process_seqs] Processed 2469684 reads in 942.042 CPU sec, 33.814 real sec
[M::process] 2315400 single-end sequences; 0 paired-end sequences
[M::process] read 2417448 sequences (280000112 bp)...
[M::mem_process_seqs] Processed 2315400 reads in 947.952 CPU sec, 34.022 real sec
[M::process] 2417448 single-end sequences; 0 paired-end sequences
[M::process] read 2293158 sequences (280000119 bp)...
[M::mem_process_seqs] Processed 2417448 reads in 939.540 CPU sec, 33.696 real sec
[M::process] 2293158 single-end sequences; 0 paired-end sequences
[M::process] read 2359046 sequences (280000015 bp)...
[M::mem_process_seqs] Processed 2293158 reads in 955.248 CPU sec, 43.709 real sec
[M::process] 2359046 single-end sequences; 0 paired-end sequences
[M::process] read 2285016 sequences (280000043 bp)...
[M::mem_process_seqs] Processed 2359046 reads in 939.296 CPU sec, 33.712 real sec
[M::process] 2285016 single-end sequences; 0 paired-end sequences
[M::process] read 2458604 sequences (280000034 bp)...
[M::mem_process_seqs] Processed 2285016 reads in 942.588 CPU sec, 33.821 real sec
[M::process] 2458604 single-end sequences; 0 paired-end sequences
[M::process] read 2409174 sequences (280000146 bp)...
[M::mem_process_seqs] Processed 2458604 reads in 971.125 CPU sec, 34.855 real sec
[M::process] 2409174 single-end sequences; 0 paired-end sequences
[M::process] read 2437318 sequences (280000254 bp)...
[M::mem_process_seqs] Processed 2409174 reads in 966.497 CPU sec, 34.669 real sec
[M::process] 2437318 single-end sequences; 0 paired-end sequences
[M::process] read 2411252 sequences (280000104 bp)...
[M::mem_process_seqs] Processed 2437318 reads in 961.193 CPU sec, 34.522 real sec
[M::process] 2411252 single-end sequences; 0 paired-end sequences
[M::process] read 2428182 sequences (280000124 bp)...
[M::mem_process_seqs] Processed 2411252 reads in 965.293 CPU sec, 34.911 real sec
[M::process] 2428182 single-end sequences; 0 paired-end sequences
[M::process] read 2373874 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2428182 reads in 955.738 CPU sec, 34.295 real sec
[M::process] 2373874 single-end sequences; 0 paired-end sequences
[M::process] read 2362146 sequences (280000010 bp)...
[M::mem_process_seqs] Processed 2373874 reads in 952.241 CPU sec, 34.163 real sec
[M::process] 2362146 single-end sequences; 0 paired-end sequences
[M::process] read 2421706 sequences (280000044 bp)...
[M::mem_process_seqs] Processed 2362146 reads in 951.610 CPU sec, 34.108 real sec
[M::process] 2421706 single-end sequences; 0 paired-end sequences
[M::process] read 2450328 sequences (280000288 bp)...
[M::mem_process_seqs] Processed 2421706 reads in 962.238 CPU sec, 45.213 real sec
[M::process] 2450328 single-end sequences; 0 paired-end sequences
[M::process] read 2357142 sequences (280000256 bp)...
[M::mem_process_seqs] Processed 2450328 reads in 956.733 CPU sec, 34.314 real sec
[M::process] 2357142 single-end sequences; 0 paired-end sequences
[M::process] read 1357308 sequences (151496137 bp)...
[M::mem_process_seqs] Processed 2357142 reads in 948.170 CPU sec, 33.997 real sec
[M::process] 1357308 single-end sequences; 0 paired-end sequences
[M::mem_process_seqs] Processed 1357308 reads in 520.214 CPU sec, 18.940 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /gscratch/srlab/programs/bwa-0.7.15/bwa mem -t 28 -R @RG\tID:Pcod1\tSM:WA\tPL:illumina\tLB:lib1\tPU:unit2 -p ./atl_cod_4_2017 ACAGCTGT_6.2_trimmed.fastq
[main] Real time: 3214.724 sec; CPU: 85881.650 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2084230 sequences (280000182 bp)...
[M::process] 2084230 single-end sequences; 0 paired-end sequences
[M::process] read 2053696 sequences (280000218 bp)...
[M::mem_process_seqs] Processed 2084230 reads in 1015.943 CPU sec, 48.117 real sec
[M::process] 2053696 single-end sequences; 0 paired-end sequences
[M::process] read 2054970 sequences (280000195 bp)...
[M::mem_process_seqs] Processed 2053696 reads in 1013.141 CPU sec, 36.412 real sec
[M::process] 2054970 single-end sequences; 0 paired-end sequences
[M::process] read 2036930 sequences (280000162 bp)...
[M::mem_process_seqs] Processed 2054970 reads in 1016.902 CPU sec, 36.465 real sec
[M::process] 2036930 single-end sequences; 0 paired-end sequences
[M::process] read 2053204 sequences (280000116 bp)...
[M::mem_process_seqs] Processed 2036930 reads in 1021.389 CPU sec, 36.635 real sec
[M::process] 2053204 single-end sequences; 0 paired-end sequences
[M::process] read 2118060 sequences (280000091 bp)...
[M::mem_process_seqs] Processed 2053204 reads in 1022.977 CPU sec, 37.865 real sec
[M::process] 2118060 single-end sequences; 0 paired-end sequences
[M::process] read 2107838 sequences (280000099 bp)...
[M::mem_process_seqs] Processed 2118060 reads in 1020.644 CPU sec, 36.674 real sec
[M::process] 2107838 single-end sequences; 0 paired-end sequences
[M::process] read 2065240 sequences (280000127 bp)...
[M::mem_process_seqs] Processed 2107838 reads in 1029.147 CPU sec, 36.901 real sec
[M::process] 2065240 single-end sequences; 0 paired-end sequences
[M::process] read 2056366 sequences (280000121 bp)...
[M::mem_process_seqs] Processed 2065240 reads in 1024.502 CPU sec, 36.740 real sec
[M::process] 2056366 single-end sequences; 0 paired-end sequences
[M::process] read 2071016 sequences (280000232 bp)...
[M::mem_process_seqs] Processed 2056366 reads in 1053.907 CPU sec, 52.093 real sec
[M::process] 2071016 single-end sequences; 0 paired-end sequences
[M::process] read 2042286 sequences (280000232 bp)...
[M::mem_process_seqs] Processed 2071016 reads in 1031.494 CPU sec, 36.963 real sec
[M::process] 2042286 single-end sequences; 0 paired-end sequences
[M::process] read 2082148 sequences (280000014 bp)...
[M::mem_process_seqs] Processed 2042286 reads in 1029.385 CPU sec, 36.882 real sec
[M::process] 2082148 single-end sequences; 0 paired-end sequences
[M::process] read 2067726 sequences (280000114 bp)...
[M::mem_process_seqs] Processed 2082148 reads in 1027.624 CPU sec, 36.828 real sec
[M::process] 2067726 single-end sequences; 0 paired-end sequences
[M::process] read 2058218 sequences (280000193 bp)...
[M::mem_process_seqs] Processed 2067726 reads in 1030.909 CPU sec, 37.021 real sec
[M::process] 2058218 single-end sequences; 0 paired-end sequences
[M::process] read 2040912 sequences (280000007 bp)...
[M::mem_process_seqs] Processed 2058218 reads in 1036.335 CPU sec, 37.145 real sec
[M::process] 2040912 single-end sequences; 0 paired-end sequences
[M::process] read 2050826 sequences (280000103 bp)...
[M::mem_process_seqs] Processed 2040912 reads in 1038.460 CPU sec, 40.007 real sec
[M::process] 2050826 single-end sequences; 0 paired-end sequences
[M::process] read 2073984 sequences (280000045 bp)...
[M::mem_process_seqs] Processed 2050826 reads in 1031.714 CPU sec, 37.014 real sec
[M::process] 2073984 single-end sequences; 0 paired-end sequences
[M::process] read 2033184 sequences (280000105 bp)...
[M::mem_process_seqs] Processed 2073984 reads in 1031.992 CPU sec, 37.014 real sec
[M::process] 2033184 single-end sequences; 0 paired-end sequences
[M::process] read 2040504 sequences (280000203 bp)...
[M::mem_process_seqs] Processed 2033184 reads in 1035.171 CPU sec, 37.117 real sec
[M::process] 2040504 single-end sequences; 0 paired-end sequences
[M::process] read 2111530 sequences (280000176 bp)...
[M::mem_process_seqs] Processed 2040504 reads in 1044.023 CPU sec, 38.520 real sec
[M::process] 2111530 single-end sequences; 0 paired-end sequences
[M::process] read 2054634 sequences (280000170 bp)...
[M::mem_process_seqs] Processed 2111530 reads in 1042.094 CPU sec, 37.579 real sec
[M::process] 2054634 single-end sequences; 0 paired-end sequences
[M::process] read 2053892 sequences (280000280 bp)...
[M::mem_process_seqs] Processed 2054634 reads in 1047.431 CPU sec, 37.555 real sec
[M::process] 2053892 single-end sequences; 0 paired-end sequences
[M::process] read 2112738 sequences (280000062 bp)...
[M::mem_process_seqs] Processed 2053892 reads in 1043.810 CPU sec, 37.439 real sec
[M::process] 2112738 single-end sequences; 0 paired-end sequences
[M::process] read 2047062 sequences (280000088 bp)...
[M::mem_process_seqs] Processed 2112738 reads in 1036.787 CPU sec, 46.894 real sec
[M::process] 2047062 single-end sequences; 0 paired-end sequences
[M::process] read 2057782 sequences (280000255 bp)...
[M::mem_process_seqs] Processed 2047062 reads in 1018.838 CPU sec, 36.531 real sec
[M::process] 2057782 single-end sequences; 0 paired-end sequences
[M::process] read 2041400 sequences (280000127 bp)...
[M::mem_process_seqs] Processed 2057782 reads in 1016.628 CPU sec, 36.459 real sec
[M::process] 2041400 single-end sequences; 0 paired-end sequences
[M::process] read 2049642 sequences (280000300 bp)...
[M::mem_process_seqs] Processed 2041400 reads in 1022.646 CPU sec, 36.656 real sec
[M::process] 2049642 single-end sequences; 0 paired-end sequences
[M::process] read 2063204 sequences (280000260 bp)...
[M::mem_process_seqs] Processed 2049642 reads in 1024.596 CPU sec, 37.757 real sec
[M::process] 2063204 single-end sequences; 0 paired-end sequences
[M::process] read 2122462 sequences (280000074 bp)...
[M::mem_process_seqs] Processed 2063204 reads in 1023.522 CPU sec, 36.707 real sec
[M::process] 2122462 single-end sequences; 0 paired-end sequences
[M::process] read 2066746 sequences (280000097 bp)...
[M::mem_process_seqs] Processed 2122462 reads in 1030.788 CPU sec, 36.982 real sec
[M::process] 2066746 single-end sequences; 0 paired-end sequences
[M::process] read 2060384 sequences (280000275 bp)...
[M::mem_process_seqs] Processed 2066746 reads in 1025.812 CPU sec, 36.788 real sec
[M::process] 2060384 single-end sequences; 0 paired-end sequences
[M::process] read 2062538 sequences (280000224 bp)...
[M::mem_process_seqs] Processed 2060384 reads in 1030.560 CPU sec, 37.002 real sec
[M::process] 2062538 single-end sequences; 0 paired-end sequences
[M::process] read 2053820 sequences (280000128 bp)...
[M::mem_process_seqs] Processed 2062538 reads in 1029.882 CPU sec, 36.918 real sec
[M::process] 2053820 single-end sequences; 0 paired-end sequences
[M::process] read 2078476 sequences (280000042 bp)...
[M::mem_process_seqs] Processed 2053820 reads in 1048.460 CPU sec, 47.792 real sec
[M::process] 2078476 single-end sequences; 0 paired-end sequences
[M::process] read 2097282 sequences (280000004 bp)...
[M::mem_process_seqs] Processed 2078476 reads in 1035.551 CPU sec, 37.173 real sec
[M::process] 2097282 single-end sequences; 0 paired-end sequences
[M::process] read 2048956 sequences (280000077 bp)...
[M::mem_process_seqs] Processed 2097282 reads in 1041.873 CPU sec, 37.364 real sec
[M::process] 2048956 single-end sequences; 0 paired-end sequences
[M::process] read 2043604 sequences (280000141 bp)...
[M::mem_process_seqs] Processed 2048956 reads in 1034.897 CPU sec, 37.116 real sec
[M::process] 2043604 single-end sequences; 0 paired-end sequences
[M::process] read 2054346 sequences (280000026 bp)...
[M::mem_process_seqs] Processed 2043604 reads in 1036.376 CPU sec, 38.294 real sec
[M::process] 2054346 single-end sequences; 0 paired-end sequences
[M::process] read 2057694 sequences (280000135 bp)...
[M::mem_process_seqs] Processed 2054346 reads in 1035.041 CPU sec, 37.151 real sec
[M::process] 2057694 single-end sequences; 0 paired-end sequences
[M::process] read 2040156 sequences (280000141 bp)...
[M::mem_process_seqs] Processed 2057694 reads in 1036.439 CPU sec, 37.160 real sec
[M::process] 2040156 single-end sequences; 0 paired-end sequences
[M::process] read 2049442 sequences (280000058 bp)...
[M::mem_process_seqs] Processed 2040156 reads in 1035.709 CPU sec, 37.154 real sec
[M::process] 2049442 single-end sequences; 0 paired-end sequences
[M::process] read 2102320 sequences (280000065 bp)...
[M::mem_process_seqs] Processed 2049442 reads in 1056.416 CPU sec, 50.356 real sec
[M::process] 2102320 single-end sequences; 0 paired-end sequences
[M::process] read 2089778 sequences (280000229 bp)...
[M::mem_process_seqs] Processed 2102320 reads in 1042.438 CPU sec, 37.365 real sec
[M::process] 2089778 single-end sequences; 0 paired-end sequences
[M::process] read 2052580 sequences (280000079 bp)...
[M::mem_process_seqs] Processed 2089778 reads in 1045.452 CPU sec, 37.497 real sec
[M::process] 2052580 single-end sequences; 0 paired-end sequences
[M::process] read 2133118 sequences (280000036 bp)...
[M::mem_process_seqs] Processed 2052580 reads in 1041.013 CPU sec, 37.378 real sec
[M::process] 2133118 single-end sequences; 0 paired-end sequences
[M::process] read 2046750 sequences (280000057 bp)...
[M::mem_process_seqs] Processed 2133118 reads in 1018.179 CPU sec, 36.518 real sec
[M::process] 2046750 single-end sequences; 0 paired-end sequences
[M::process] read 2042512 sequences (280000056 bp)...
[M::mem_process_seqs] Processed 2046750 reads in 1027.761 CPU sec, 36.861 real sec
[M::process] 2042512 single-end sequences; 0 paired-end sequences
[M::process] read 2028332 sequences (280000045 bp)...
[M::mem_process_seqs] Processed 2042512 reads in 1021.561 CPU sec, 36.887 real sec
[M::process] 2028332 single-end sequences; 0 paired-end sequences
[M::process] read 2031054 sequences (280000058 bp)...
[M::mem_process_seqs] Processed 2028332 reads in 1021.914 CPU sec, 36.713 real sec
[M::process] 2031054 single-end sequences; 0 paired-end sequences
[M::process] read 2089430 sequences (280000216 bp)...
[M::mem_process_seqs] Processed 2031054 reads in 1039.871 CPU sec, 46.197 real sec
[M::process] 2089430 single-end sequences; 0 paired-end sequences
[M::process] read 2108060 sequences (280000161 bp)...
[M::mem_process_seqs] Processed 2089430 reads in 1064.140 CPU sec, 38.163 real sec
[M::process] 2108060 single-end sequences; 0 paired-end sequences
[M::process] read 2061416 sequences (280000013 bp)...
[M::mem_process_seqs] Processed 2108060 reads in 1039.569 CPU sec, 37.308 real sec
[M::process] 2061416 single-end sequences; 0 paired-end sequences
[M::process] read 2071846 sequences (280000083 bp)...
[M::mem_process_seqs] Processed 2061416 reads in 1042.312 CPU sec, 37.396 real sec
[M::process] 2071846 single-end sequences; 0 paired-end sequences
[M::process] read 2078658 sequences (280000030 bp)...
[M::mem_process_seqs] Processed 2071846 reads in 1060.020 CPU sec, 40.440 real sec
[M::process] 2078658 single-end sequences; 0 paired-end sequences
[M::process] read 2067120 sequences (280000031 bp)...
[M::mem_process_seqs] Processed 2078658 reads in 1062.467 CPU sec, 38.125 real sec
[M::process] 2067120 single-end sequences; 0 paired-end sequences
[M::process] read 2074900 sequences (280000034 bp)...
[M::mem_process_seqs] Processed 2067120 reads in 1063.585 CPU sec, 38.134 real sec
[M::process] 2074900 single-end sequences; 0 paired-end sequences
[M::process] read 2083376 sequences (280000185 bp)...
[M::mem_process_seqs] Processed 2074900 reads in 1046.492 CPU sec, 37.551 real sec
[M::process] 2083376 single-end sequences; 0 paired-end sequences
[M::process] read 2062836 sequences (280000040 bp)...
[M::mem_process_seqs] Processed 2083376 reads in 1033.470 CPU sec, 37.789 real sec
[M::process] 2062836 single-end sequences; 0 paired-end sequences
[M::process] read 2034952 sequences (280000004 bp)...
[M::mem_process_seqs] Processed 2062836 reads in 1035.722 CPU sec, 37.182 real sec
[M::process] 2034952 single-end sequences; 0 paired-end sequences
[M::process] read 2057232 sequences (280000077 bp)...
[M::mem_process_seqs] Processed 2034952 reads in 1043.623 CPU sec, 37.407 real sec
[M::process] 2057232 single-end sequences; 0 paired-end sequences
[M::process] read 2066964 sequences (280000162 bp)...
[M::mem_process_seqs] Processed 2057232 reads in 1058.556 CPU sec, 37.958 real sec
[M::process] 2066964 single-end sequences; 0 paired-end sequences
[M::process] read 2040082 sequences (280000175 bp)...
[M::mem_process_seqs] Processed 2066964 reads in 1069.939 CPU sec, 46.880 real sec
[M::process] 2040082 single-end sequences; 0 paired-end sequences
[M::process] read 2087176 sequences (280000024 bp)...
[M::mem_process_seqs] Processed 2040082 reads in 1052.548 CPU sec, 37.728 real sec
[M::process] 2087176 single-end sequences; 0 paired-end sequences
[M::process] read 2163424 sequences (280000061 bp)...
[M::mem_process_seqs] Processed 2087176 reads in 1075.694 CPU sec, 39.235 real sec
[M::process] 2163424 single-end sequences; 0 paired-end sequences
[M::process] read 2029650 sequences (280000135 bp)...
[M::mem_process_seqs] Processed 2163424 reads in 1061.444 CPU sec, 38.105 real sec
[M::process] 2029650 single-end sequences; 0 paired-end sequences
[M::process] read 2045510 sequences (280000243 bp)...
[M::mem_process_seqs] Processed 2029650 reads in 1030.750 CPU sec, 36.957 real sec
[M::process] 2045510 single-end sequences; 0 paired-end sequences
[M::process] read 2107462 sequences (280000183 bp)...
[M::mem_process_seqs] Processed 2045510 reads in 1031.160 CPU sec, 37.006 real sec
[M::process] 2107462 single-end sequences; 0 paired-end sequences
[M::process] read 2047360 sequences (280000188 bp)...
[M::mem_process_seqs] Processed 2107462 reads in 1009.036 CPU sec, 36.176 real sec
[M::process] 2047360 single-end sequences; 0 paired-end sequences
[M::process] read 2055568 sequences (280000042 bp)...
[M::mem_process_seqs] Processed 2047360 reads in 1014.501 CPU sec, 36.378 real sec
[M::process] 2055568 single-end sequences; 0 paired-end sequences
[M::process] read 2032616 sequences (280000111 bp)...
[M::mem_process_seqs] Processed 2055568 reads in 1021.284 CPU sec, 36.642 real sec
[M::process] 2032616 single-end sequences; 0 paired-end sequences
[M::process] read 2035460 sequences (280000118 bp)...
[M::mem_process_seqs] Processed 2032616 reads in 1024.331 CPU sec, 36.710 real sec
[M::process] 2035460 single-end sequences; 0 paired-end sequences
[M::process] read 2094024 sequences (280000072 bp)...
[M::mem_process_seqs] Processed 2035460 reads in 1020.073 CPU sec, 44.491 real sec
[M::process] 2094024 single-end sequences; 0 paired-end sequences
[M::process] read 2085806 sequences (280000049 bp)...
[M::mem_process_seqs] Processed 2094024 reads in 1022.129 CPU sec, 36.671 real sec
[M::process] 2085806 single-end sequences; 0 paired-end sequences
[M::process] read 2077310 sequences (280000200 bp)...
[M::mem_process_seqs] Processed 2085806 reads in 1015.096 CPU sec, 36.373 real sec
[M::process] 2077310 single-end sequences; 0 paired-end sequences
[M::process] read 2037866 sequences (280000014 bp)...
[M::mem_process_seqs] Processed 2077310 reads in 1017.693 CPU sec, 36.452 real sec
[M::process] 2037866 single-end sequences; 0 paired-end sequences
[M::process] read 2043790 sequences (280000253 bp)...
[M::mem_process_seqs] Processed 2037866 reads in 1017.221 CPU sec, 36.507 real sec
[M::process] 2043790 single-end sequences; 0 paired-end sequences
[M::process] read 2032364 sequences (280000096 bp)...
[M::mem_process_seqs] Processed 2043790 reads in 1016.746 CPU sec, 36.461 real sec
[M::process] 2032364 single-end sequences; 0 paired-end sequences
[M::process] read 2078000 sequences (280000240 bp)...
[M::mem_process_seqs] Processed 2032364 reads in 1030.509 CPU sec, 36.980 real sec
[M::process] 2078000 single-end sequences; 0 paired-end sequences
[M::process] read 2074478 sequences (280000218 bp)...
[M::mem_process_seqs] Processed 2078000 reads in 1027.029 CPU sec, 36.829 real sec
[M::process] 2074478 single-end sequences; 0 paired-end sequences
[M::process] read 2065440 sequences (280000021 bp)...
[M::mem_process_seqs] Processed 2074478 reads in 1040.941 CPU sec, 37.315 real sec
[M::process] 2065440 single-end sequences; 0 paired-end sequences
[M::process] read 2058768 sequences (280000068 bp)...
[M::mem_process_seqs] Processed 2065440 reads in 1058.952 CPU sec, 37.971 real sec
[M::process] 2058768 single-end sequences; 0 paired-end sequences
[M::process] read 2066176 sequences (280000051 bp)...
[M::mem_process_seqs] Processed 2058768 reads in 1045.334 CPU sec, 41.759 real sec
[M::process] 2066176 single-end sequences; 0 paired-end sequences
[M::process] read 2065676 sequences (280000162 bp)...
[M::mem_process_seqs] Processed 2066176 reads in 1027.483 CPU sec, 36.823 real sec
[M::process] 2065676 single-end sequences; 0 paired-end sequences
[M::process] read 2051096 sequences (280000170 bp)...
[M::mem_process_seqs] Processed 2065676 reads in 1028.226 CPU sec, 36.852 real sec
[M::process] 2051096 single-end sequences; 0 paired-end sequences
[M::process] read 2059384 sequences (280000268 bp)...
[M::mem_process_seqs] Processed 2051096 reads in 1028.684 CPU sec, 36.903 real sec
[M::process] 2059384 single-end sequences; 0 paired-end sequences
[M::process] read 2122678 sequences (280000202 bp)...
[M::mem_process_seqs] Processed 2059384 reads in 1030.340 CPU sec, 37.176 real sec
[M::process] 2122678 single-end sequences; 0 paired-end sequences
[M::process] read 2055882 sequences (280000278 bp)...
[M::mem_process_seqs] Processed 2122678 reads in 1031.582 CPU sec, 37.015 real sec
[M::process] 2055882 single-end sequences; 0 paired-end sequences
[M::process] read 1394197 sequences (185124735 bp)...
[M::mem_process_seqs] Processed 2055882 reads in 1025.256 CPU sec, 36.739 real sec
[M::process] 1394197 single-end sequences; 0 paired-end sequences
[M::mem_process_seqs] Processed 1394197 reads in 684.271 CPU sec, 24.698 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /gscratch/srlab/programs/bwa-0.7.15/bwa mem -t 28 -R @RG\tID:Pcod1\tSM:AD\tPL:illumina\tLB:lib1\tPU:unit1 -p ./atl_cod_4_2017 GGTCAGTT_6.1_trimmed.fastq
[main] Real time: 3379.298 sec; CPU: 90720.997 sec
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2424814 sequences (280000131 bp)...
[M::process] 2424814 single-end sequences; 0 paired-end sequences
[M::process] read 2345754 sequences (280000024 bp)...
[M::mem_process_seqs] Processed 2424814 reads in 987.725 CPU sec, 47.747 real sec
[M::process] 2345754 single-end sequences; 0 paired-end sequences
[M::process] read 2304062 sequences (280000151 bp)...
[M::mem_process_seqs] Processed 2345754 reads in 987.966 CPU sec, 35.432 real sec
[M::process] 2304062 single-end sequences; 0 paired-end sequences
[M::process] read 2300694 sequences (280000216 bp)...
[M::mem_process_seqs] Processed 2304062 reads in 994.207 CPU sec, 35.677 real sec
[M::process] 2300694 single-end sequences; 0 paired-end sequences
[M::process] read 2397586 sequences (280000045 bp)...
[M::mem_process_seqs] Processed 2300694 reads in 990.953 CPU sec, 35.609 real sec
[M::process] 2397586 single-end sequences; 0 paired-end sequences
[M::process] read 2373346 sequences (280000023 bp)...
[M::mem_process_seqs] Processed 2397586 reads in 1002.650 CPU sec, 35.964 real sec
[M::process] 2373346 single-end sequences; 0 paired-end sequences
[M::process] read 2398278 sequences (280000282 bp)...
[M::mem_process_seqs] Processed 2373346 reads in 1000.379 CPU sec, 35.882 real sec
[M::process] 2398278 single-end sequences; 0 paired-end sequences
[M::process] read 2299976 sequences (280000032 bp)...
[M::mem_process_seqs] Processed 2398278 reads in 1001.640 CPU sec, 35.935 real sec
[M::process] 2299976 single-end sequences; 0 paired-end sequences
[M::process] read 2317710 sequences (280000074 bp)...
[M::mem_process_seqs] Processed 2299976 reads in 1008.325 CPU sec, 36.167 real sec
[M::process] 2317710 single-end sequences; 0 paired-end sequences
[M::process] read 2402508 sequences (280000056 bp)...
[M::mem_process_seqs] Processed 2317710 reads in 1019.419 CPU sec, 49.658 real sec
[M::process] 2402508 single-end sequences; 0 paired-end sequences
[M::process] read 2327734 sequences (280000209 bp)...
[M::mem_process_seqs] Processed 2402508 reads in 1007.259 CPU sec, 36.135 real sec
[M::process] 2327734 single-end sequences; 0 paired-end sequences
[M::process] read 2374626 sequences (280000210 bp)...
[M::mem_process_seqs] Processed 2327734 reads in 1011.107 CPU sec, 36.287 real sec
[M::process] 2374626 single-end sequences; 0 paired-end sequences
[M::process] read 2301236 sequences (280000115 bp)...
[M::mem_process_seqs] Processed 2374626 reads in 1016.072 CPU sec, 36.475 real sec
[M::process] 2301236 single-end sequences; 0 paired-end sequences
[M::process] read 2362688 sequences (280000180 bp)...
[M::mem_process_seqs] Processed 2301236 reads in 1017.190 CPU sec, 36.511 real sec
[M::process] 2362688 single-end sequences; 0 paired-end sequences
[M::process] read 2294222 sequences (280000126 bp)...
[M::mem_process_seqs] Processed 2362688 reads in 1022.439 CPU sec, 36.674 real sec
[M::process] 2294222 single-end sequences; 0 paired-end sequences
[M::process] read 2426168 sequences (280000039 bp)...
[M::mem_process_seqs] Processed 2294222 reads in 1016.727 CPU sec, 36.459 real sec
[M::process] 2426168 single-end sequences; 0 paired-end sequences
[M::process] read 2388698 sequences (280000016 bp)...
[M::mem_process_seqs] Processed 2426168 reads in 1016.180 CPU sec, 36.661 real sec
[M::process] 2388698 single-end sequences; 0 paired-end sequences
[M::process] read 2362710 sequences (280000040 bp)...
[M::mem_process_seqs] Processed 2388698 reads in 1021.599 CPU sec, 36.660 real sec
[M::process] 2362710 single-end sequences; 0 paired-end sequences
[M::process] read 2394942 sequences (280000229 bp)...
[M::mem_process_seqs] Processed 2362710 reads in 1025.587 CPU sec, 36.806 real sec
[M::process] 2394942 single-end sequences; 0 paired-end sequences
[M::process] read 2319064 sequences (280000266 bp)...
[M::mem_process_seqs] Processed 2394942 reads in 1012.139 CPU sec, 52.825 real sec
[M::process] 2319064 single-end sequences; 0 paired-end sequences
[M::process] read 2313808 sequences (280000038 bp)...
[M::mem_process_seqs] Processed 2319064 reads in 986.186 CPU sec, 35.403 real sec
[M::process] 2313808 single-end sequences; 0 paired-end sequences
[M::process] read 2298718 sequences (280000019 bp)...
[M::mem_process_seqs] Processed 2313808 reads in 993.575 CPU sec, 35.616 real sec
[M::process] 2298718 single-end sequences; 0 paired-end sequences
[M::process] read 2343602 sequences (280000008 bp)...
[M::mem_process_seqs] Processed 2298718 reads in 1001.470 CPU sec, 35.979 real sec
[M::process] 2343602 single-end sequences; 0 paired-end sequences
[M::process] read 2365198 sequences (280000223 bp)...
[M::mem_process_seqs] Processed 2343602 reads in 1001.256 CPU sec, 36.031 real sec
[M::process] 2365198 single-end sequences; 0 paired-end sequences
[M::process] read 2349320 sequences (280000012 bp)...
[M::mem_process_seqs] Processed 2365198 reads in 1001.905 CPU sec, 35.937 real sec
[M::process] 2349320 single-end sequences; 0 paired-end sequences
[M::process] read 2307390 sequences (280000091 bp)...
[M::mem_process_seqs] Processed 2349320 reads in 1002.571 CPU sec, 35.989 real sec
[M::process] 2307390 single-end sequences; 0 paired-end sequences
[M::process] read 2311308 sequences (280000217 bp)...
[M::mem_process_seqs] Processed 2307390 reads in 1001.136 CPU sec, 35.899 real sec
[M::process] 2311308 single-end sequences; 0 paired-end sequences
[M::process] read 2457352 sequences (280000021 bp)...
[M::mem_process_seqs] Processed 2311308 reads in 1032.755 CPU sec, 49.918 real sec
[M::process] 2457352 single-end sequences; 0 paired-end sequences
[M::process] read 2337238 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2457352 reads in 1002.571 CPU sec, 35.978 real sec
[M::process] 2337238 single-end sequences; 0 paired-end sequences
[M::process] read 2376726 sequences (280000210 bp)...
[M::mem_process_seqs] Processed 2337238 reads in 1008.097 CPU sec, 36.185 real sec
[M::process] 2376726 single-end sequences; 0 paired-end sequences
[M::process] read 2331238 sequences (280000161 bp)...
[M::mem_process_seqs] Processed 2376726 reads in 1009.365 CPU sec, 36.263 real sec
[M::process] 2331238 single-end sequences; 0 paired-end sequences
[M::process] read 2347068 sequences (280000001 bp)...
[M::mem_process_seqs] Processed 2331238 reads in 1009.029 CPU sec, 36.241 real sec
[M::process] 2347068 single-end sequences; 0 paired-end sequences
[M::process] read 2310258 sequences (280000103 bp)...
[M::mem_process_seqs] Processed 2347068 reads in 1009.373 CPU sec, 36.237 real sec
[M::process] 2310258 single-end sequences; 0 paired-end sequences
[M::process] read 2442988 sequences (280000175 bp)...
[M::mem_process_seqs] Processed 2310258 reads in 1006.312 CPU sec, 36.144 real sec
[M::process] 2442988 single-end sequences; 0 paired-end sequences
[M::process] read 2404094 sequences (280000094 bp)...
[M::mem_process_seqs] Processed 2442988 reads in 1011.902 CPU sec, 36.352 real sec
[M::process] 2404094 single-end sequences; 0 paired-end sequences
[M::process] read 2397738 sequences (280000082 bp)...
[M::mem_process_seqs] Processed 2404094 reads in 1026.017 CPU sec, 36.815 real sec
[M::process] 2397738 single-end sequences; 0 paired-end sequences
[M::process] read 2534748 sequences (280000190 bp)...
[M::mem_process_seqs] Processed 2397738 reads in 1016.650 CPU sec, 36.647 real sec
[M::process] 2534748 single-end sequences; 0 paired-end sequences
[M::process] read 2382722 sequences (280000156 bp)...
[M::mem_process_seqs] Processed 2534748 reads in 1021.083 CPU sec, 52.906 real sec
[M::process] 2382722 single-end sequences; 0 paired-end sequences
[M::process] read 2362004 sequences (280000005 bp)...
[M::mem_process_seqs] Processed 2382722 reads in 995.036 CPU sec, 35.699 real sec
[M::process] 2362004 single-end sequences; 0 paired-end sequences
[M::process] read 2360340 sequences (280000089 bp)...
[M::mem_process_seqs] Processed 2362004 reads in 995.405 CPU sec, 35.717 real sec
[M::process] 2360340 single-end sequences; 0 paired-end sequences
[M::process] read 2523426 sequences (280000022 bp)...
[M::mem_process_seqs] Processed 2360340 reads in 1049.000 CPU sec, 37.633 real sec
[M::process] 2523426 single-end sequences; 0 paired-end sequences
[M::process] read 2472820 sequences (280000252 bp)...
[M::mem_process_seqs] Processed 2523426 reads in 1018.086 CPU sec, 37.104 real sec
[M::process] 2472820 single-end sequences; 0 paired-end sequences
[M::process] read 2414144 sequences (280000226 bp)...
[M::mem_process_seqs] Processed 2472820 reads in 1034.066 CPU sec, 37.091 real sec
[M::process] 2414144 single-end sequences; 0 paired-end sequences
[M::process] read 2534770 sequences (280000016 bp)...
[M::mem_process_seqs] Processed 2414144 reads in 1025.091 CPU sec, 36.851 real sec
[M::process] 2534770 single-end sequences; 0 paired-end sequences
[M::process] read 2333738 sequences (280000183 bp)...
[M::mem_process_seqs] Processed 2534770 reads in 1036.515 CPU sec, 37.189 real sec
[M::process] 2333738 single-end sequences; 0 paired-end sequences
[M::process] read 2444094 sequences (280000052 bp)...
[M::mem_process_seqs] Processed 2333738 reads in 1009.279 CPU sec, 36.247 real sec
[M::process] 2444094 single-end sequences; 0 paired-end sequences
[M::process] read 2413120 sequences (280000192 bp)...
[M::mem_process_seqs] Processed 2444094 reads in 1023.824 CPU sec, 36.738 real sec
[M::process] 2413120 single-end sequences; 0 paired-end sequences
[M::process] read 2395502 sequences (280000221 bp)...
[M::mem_process_seqs] Processed 2413120 reads in 1054.501 CPU sec, 52.371 real sec
[M::process] 2395502 single-end sequences; 0 paired-end sequences
[M::process] read 2557156 sequences (280000093 bp)...
[M::mem_process_seqs] Processed 2395502 reads in 1056.329 CPU sec, 37.947 real sec
[M::process] 2557156 single-end sequences; 0 paired-end sequences
[M::process] read 2404132 sequences (280000033 bp)...
[M::mem_process_seqs] Processed 2557156 reads in 1080.514 CPU sec, 38.781 real sec
[M::process] 2404132 single-end sequences; 0 paired-end sequences
[M::process] read 2477592 sequences (280000244 bp)...
[M::mem_process_seqs] Processed 2404132 reads in 1039.772 CPU sec, 37.341 real sec
[M::process] 2477592 single-end sequences; 0 paired-end sequences
[M::process] read 2492538 sequences (280000111 bp)...
[M::mem_process_seqs] Processed 2477592 reads in 1048.053 CPU sec, 37.877 real sec
[M::process] 2492538 single-end sequences; 0 paired-end sequences
[M::process] read 2487892 sequences (280000040 bp)...
[M::mem_process_seqs] Processed 2492538 reads in 1030.617 CPU sec, 36.988 real sec
[M::process] 2487892 single-end sequences; 0 paired-end sequences
[M::process] read 2514710 sequences (280000033 bp)...
[M::mem_process_seqs] Processed 2487892 reads in 1022.099 CPU sec, 36.669 real sec
[M::process] 2514710 single-end sequences; 0 paired-end sequences
[M::process] read 2394846 sequences (280000013 bp)...
[M::mem_process_seqs] Processed 2514710 reads in 995.728 CPU sec, 36.051 real sec
[M::process] 2394846 single-end sequences; 0 paired-end sequences
[M::process] read 2371390 sequences (280000108 bp)...
[M::mem_process_seqs] Processed 2394846 reads in 988.731 CPU sec, 35.508 real sec
[M::process] 2371390 single-end sequences; 0 paired-end sequences
[M::process] read 2335226 sequences (280000114 bp)...
[M::mem_process_seqs] Processed 2371390 reads in 1015.201 CPU sec, 36.425 real sec
[M::process] 2335226 single-end sequences; 0 paired-end sequences
[M::process] read 2477980 sequences (280000162 bp)...
[M::mem_process_seqs] Processed 2335226 reads in 1026.616 CPU sec, 37.153 real sec
[M::process] 2477980 single-end sequences; 0 paired-end sequences
[M::process] read 2354754 sequences (280000200 bp)...
[M::mem_process_seqs] Processed 2477980 reads in 1002.520 CPU sec, 35.987 real sec
[M::process] 2354754 single-end sequences; 0 paired-end sequences
[M::process] read 2383172 sequences (280000262 bp)...
[M::mem_process_seqs] Processed 2354754 reads in 1003.100 CPU sec, 36.010 real sec
[M::process] 2383172 single-end sequences; 0 paired-end sequences
[M::process] read 2408390 sequences (280000174 bp)...
[M::mem_process_seqs] Processed 2383172 reads in 997.315 CPU sec, 35.786 real sec
[M::process] 2408390 single-end sequences; 0 paired-end sequences
[M::process] read 2316684 sequences (280000028 bp)...
[M::mem_process_seqs] Processed 2408390 reads in 1000.671 CPU sec, 37.474 real sec
[M::process] 2316684 single-end sequences; 0 paired-end sequences
[M::process] read 2508560 sequences (280000037 bp)...
[M::mem_process_seqs] Processed 2316684 reads in 1006.243 CPU sec, 36.104 real sec
[M::process] 2508560 single-end sequences; 0 paired-end sequences
[M::process] read 2477400 sequences (280000090 bp)...
[M::mem_process_seqs] Processed 2508560 reads in 1032.602 CPU sec, 37.019 real sec
[M::process] 2477400 single-end sequences; 0 paired-end sequences
[M::process] read 2438554 sequences (280000087 bp)...
[M::mem_process_seqs] Processed 2477400 reads in 1025.677 CPU sec, 36.828 real sec
[M::process] 2438554 single-end sequences; 0 paired-end sequences
[M::process] read 2513654 sequences (280000151 bp)...
[M::mem_process_seqs] Processed 2438554 reads in 1031.997 CPU sec, 37.103 real sec
[M::process] 2513654 single-end sequences; 0 paired-end sequences
[M::process] read 2383164 sequences (280000017 bp)...
[M::mem_process_seqs] Processed 2513654 reads in 1015.919 CPU sec, 36.471 real sec
[M::process] 2383164 single-end sequences; 0 paired-end sequences
[M::process] read 2416006 sequences (280000287 bp)...
[M::mem_process_seqs] Processed 2383164 reads in 1018.304 CPU sec, 36.545 real sec
[M::process] 2416006 single-end sequences; 0 paired-end sequences
[M::process] read 2476052 sequences (280000039 bp)...
[M::mem_process_seqs] Processed 2416006 reads in 1012.766 CPU sec, 36.369 real sec
[M::process] 2476052 single-end sequences; 0 paired-end sequences
[M::process] read 2479402 sequences (280000251 bp)...
[M::mem_process_seqs] Processed 2476052 reads in 1019.695 CPU sec, 36.894 real sec
[M::process] 2479402 single-end sequences; 0 paired-end sequences
[M::process] read 195904 sequences (22872720 bp)...
[M::mem_process_seqs] Processed 2479402 reads in 1010.283 CPU sec, 36.293 real sec
[M::process] 195904 single-end sequences; 0 paired-end sequences
[M::mem_process_seqs] Processed 195904 reads in 87.918 CPU sec, 3.342 real sec
[main] Version: 0.7.15-r1140
[main] CMD: /gscratch/srlab/programs/bwa-0.7.15/bwa mem -t 28 -R @RG\tID:Pcod1\tSM:AD\tPL:illumina\tLB:lib1\tPU:unit2 -p ./atl_cod_4_2017 GGTCAGTT_6.2_trimmed.fastq
[main] Real time: 2668.980 sec; CPU: 71154.488 sec