Warning: Permanently added 'qi0037.hpc.bcgsc.bc.ca,10.9.228.173' (RSA) to the list of known hosts.
warning: discarded 74334 reads shorter than 30 bases
warning: discarded 116475 unchaste reads
warning: discarded 5553 reads containing non-ACGT characters
Reading `HS1780-1.fa'...
Read 9592 contigs
Vertices: 9592 Edges: 28268
Bubbles: 209 Popped: 185 Too long: 24
Reading `HS1780-3.fa'...
Read 9407 contigs
Vertices: 9407 Edges: 27528
Reading target `HS1780-3.fa'...
Reading from standard input...
Read 2267482 bases, 9407 contigs, 9407 scaffolds from `HS1780-3.fa'. Expecting 1994679 k-mer.
Reading target `HS1780-3.fa'...
Read 9407 contigs. Hash load: 1994679 / 16777216 = 0.118892
Reading `/projects/NBL/assemblies/targeted/NBL01/HS1780.sam.gz'...
Read 54 alignments. Hash load: 54 / 97 = 0.556701
Read 100 alignments. Hash load: 98 / 193 = 0.507772
Read 202 alignments. Hash load: 194 / 389 = 0.498715
Read 210326 alignments. Hash load: 390 / 769 = 0.507152
Read 261734 alignments. Hash load: 770 / 1543 = 0.499028
Read 656568 alignments. Hash load: 1544 / 3079 = 0.501462
Aligned 1000000 reads
Read 1000000 alignments. Hash load: 1692 / 3079 = 0.549529
Read 1945622 alignments. Hash load: 3080 / 6151 = 0.500732
Aligned 2000000 reads
Read 2000000 alignments. Hash load: 1650 / 6151 = 0.268249
Aligned 3000000 reads
Read 3000000 alignments. Hash load: 2300 / 6151 = 0.373923
Aligned 3479846 of 3611758 reads (96.3477%)
Read 3611758 alignments
Mateless      1576  0.0872%
Unaligned     3451  0.191%
Singleton   124968  6.92%
FR         1184338  65.6%
RF               1  5.54e-05%
FF             292  0.0162%
Different   470876  26.1%
Multimap        78  0.00432%
Split        21087  1.17%
Total      1806667
Stats mean: 401.5 median: 403 sd: 40.65 n: 1184223 min: 74 max: 529
                                        ___▁▁▂▃▃▄▅▆▇▇█████▇▇▆▅▄▃▂▁▁__       
Stats mean: 401.5 median: 403 sd: 40.65 n: 1184223 min: 74 max: 529
                                        ___▁▁▂▃▃▄▅▆▇▇█████▇▇▆▅▄▃▂▁▁__       
warning: overlap does not agree with estimate
	4314-,1122+ -22 4314-,28,17,9.9
warning: overlap does not agree with estimate
	8318-,4469+ -5 8318-,-28,62,5.2
warning: overlap does not agree with estimate
	8918+,8016+ -19 8918+,8,90,4.3
Reading `HS1780-4.fa'...
Read 9551 contigs
Vertices: 9551 Edges: 28104
Reading `HS1780-4.path2'...
Total number of paths: 393
The minimum coverage of single-end contigs is 6.16667.
The minimum coverage of merged contigs is 6.85714.
Consider increasing the coverage threshold parameter, c, to 6.85714.