 Trying the A5_pipeline script
[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=8RS_CAGATC_L005_R1_illuminaformat_sed.fastq
      p2=8RS_CAGATC_L005_R2_illuminaformat_sed.fastq
[a5] Cleaning reads with SGA
16429824
[a5] Found 1 libraries
[a5] Starting pipeline at step 1
[a5] Cleaning reads with SGA
preprocess: WARNING - it is suggested that the min read length is 40
preprocess: Using very short reads may considerably impact the performance
Parameters:
QualTrim: 10
QualFilter: at most 20 low quality bases
HardClip: 0
Min length: 29
Sample freq: 1
PE Mode: 0
Quality scaling: 3
MinGC: 0
MaxGC: 1
Outfile: stdout
Discarding sequences with ambiguous bases
Processing 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq

Processing 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq

Warning, read @HWI-ST705:113:C026NACX has no sequence or quality values

Preprocess stats:
Reads parsed:	40309497
Reads kept:	40146240 (0.99595)
Reads failed primer screen:	9995 (0.000247956)
Bases parsed:	4071259197
Bases kept:	3853581516 (0.946533)
Number of incorrectly paired reads that were discarded: 0
[timer - sga preprocess] wall clock: 501.47s CPU: 260.85s
[a5] sga index -d 8214912 -t 4 8RS_CAGATC_L005_outputFile_A5.s1/8RS_CAGATC_L005_outputFile_A5.pp.fastq > 8RS_CAGATC_L005_outputFile_A5.s1/index.out 2> 8RS_CAGATC_L005_outputFile_A5.s1/index.err
[a5] sga correct -t 4 -o 8RS_CAGATC_L005_outputFile_A5.s1/8RS_CAGATC_L005_outputFile_A5.pp.ec.fa 8RS_CAGATC_L005_outputFile_A5.s1/8RS_CAGATC_L005_outputFile_A5.pp.fastq > 8RS_CAGATC_L005_outputFile_A5.s1/correct.out
[timer - sga::correct] wall clock: 10454.69s CPU: 24849.96s
Use of uninitialized value in concatenation (.) or string at ./a5_pipeline.pl line 321, <FQ> line 1.
In fix_read_id, got id 
[a5] perl -p -i -e "s/^([@\+])(.+)\n/\$1\$2\/1\n/g" 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq
Use of uninitialized value in concatenation (.) or string at ./a5_pipeline.pl line 321, <FQ> line 2.
In fix_read_id, got id 
[a5] perl -p -i -e "s/^([@\+])(.+)\n/\$1\$2\/2\n/g" 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/sga preprocess -q 10 -f 20 -m 29 --pe-mode=1 --phred64  8RS_CAGATC_L005_R1_illuminaformat_sed.fastq 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq > 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp
preprocess: WARNING - it is suggested that the min read length is 40
preprocess: Using very short reads may considerably impact the performance
Parameters:
QualTrim: 10
QualFilter: at most 20 low quality bases
HardClip: 0
Min length: 29
Sample freq: 1
PE Mode: 1
Quality scaling: 3
MinGC: 0
MaxGC: 1
Outfile: stdout
Discarding sequences with ambiguous bases
Processing pe files 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq, 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq
Warning, read @HWI-ST705:113:C026NACX/2 has no sequence or quality values

Preprocess stats:
Reads parsed:	2199474
Reads kept:	2103282 (0.956266)
Reads failed primer screen:	9447 (0.00429512)
Bases parsed:	222146874
Bases kept:	200521490 (0.902653)
Number of incorrectly paired reads that were discarded: 0
[timer - sga preprocess] wall clock: 18.93s CPU: 12.02s
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/sga correct -t 4 -p 8RS_CAGATC_L005_outputFile_A5.pp -o 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp.ec.fastq 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp > 8RS_CAGATC_L005_outputFile_A5.s1/raw1.correct.out
[timer - sga::correct] wall clock: 542.24s CPU: 1263.20s
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/tagdust -s /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/../adapter.fasta -o 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp.ec.tagdust.fastq 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp.ec.fastq
TagDust version 1.13, Copyright (C) 2009 Timo Lassmann <timolassmann@gmail.com>
Creating Library
Generating Background
101	done	(1487253)
100	done	(26052)
99	done	(33615)
98	done	(36828)
97	done	(34800)
96	done	(30070)
95	done	(27406)
94	done	(25129)
93	done	(21454)
92	done	(18986)
91	done	(17815)
90	done	(16430)
89	done	(14857)
88	done	(14060)
87	done	(12985)
86	done	(12629)
85	done	(11698)
84	done	(10430)
83	done	(10323)
82	done	(9778)
81	done	(9473)
80	done	(9014)
79	done	(8333)
78	done	(7772)
77	done	(7460)
76	done	(6807)
75	done	(8511)
74	done	(7570)
73	done	(7564)
72	done	(7031)
71	done	(6854)
70	done	(6460)
69	done	(6091)
68	done	(5864)
67	done	(5879)
66	done	(5357)
65	done	(5304)
64	done	(5004)
63	done	(5008)
62	done	(4864)
61	done	(4593)
60	done	(4476)
59	done	(4196)
58	done	(3982)
57	done	(3949)
56	done	(3826)
55	done	(3753)
54	done	(3321)
53	done	(3248)
52	done	(3041)
51	done	(2569)
50	done	(3462)
49	done	(3393)
48	done	(3219)
47	done	(2996)
46	done	(2859)
45	done	(2912)
44	done	(2751)
43	done	(2685)
42	done	(2595)
41	done	(2587)
40	done	(2517)
39	done	(2349)
38	done	(2263)
37	done	(2143)
36	done	(2033)
35	done	(2058)
34	done	(2060)
33	done	(1830)
32	done	(1834)
31	done	(1740)
30	done	(1636)
29	done	(1587)

2103281	Sequences
6350	Tags rejected (0.3%) at 34.0% coverage cutoff (0.010000 FDR).


	Elapsed time:
	     70 seconds (62.82 CPU+SYS seconds)
[a5] tagdust -s -o 8RS_CAGATC_L005_outputFile_A5.s1/8RS_CAGATC_L005_outputFile_A5.dusted.fq /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/../adapter.fasta 8RS_CAGATC_L005_outputFile_A5.s1/8RS_CAGATC_L005_outputFile_A5.pp.ec.fa
TagDust version 1.13, Copyright (C) 2009 Timo Lassmann <timolassmann@gmail.com>
Creating Library
Generating Background
101	done	(29468012)
100	done	(507055)
99	done	(605445)
98	done	(664688)
97	done	(619153)
96	done	(568532)
95	done	(522106)
94	done	(470961)
93	done	(379616)
92	done	(336307)
91	done	(308176)
90	done	(276166)
89	done	(258541)
88	done	(229515)
87	done	(210950)
86	done	(200370)
85	done	(182142)
84	done	(173635)
83	done	(161105)
82	done	(154330)
81	done	(145409)
80	done	(134316)
79	done	(118575)
78	done	(104090)
77	done	(85787)
76	done	(73169)
75	done	(137160)
74	done	(132503)
73	done	(131513)
72	done	(124194)
71	done	(119782)
70	done	(116616)
69	done	(110375)
68	done	(106867)
67	done	(103262)
66	done	(99487)
65	done	(96239)
64	done	(92266)
63	done	(89382)
62	done	(87535)
61	done	(84643)
60	done	(81557)
59	done	(79232)
58	done	(76350)
57	done	(75508)
56	done	(72510)
55	done	(70063)
54	done	(67324)
53	done	(65987)
52	done	(64051)
51	done	(61682)
50	done	(59242)
49	done	(56323)
48	done	(55676)
47	done	(53465)
46	done	(50832)
45	done	(48424)
44	done	(45800)
43	done	(44162)
42	done	(41858)
41	done	(40503)
40	done	(37899)
39	done	(37501)
38	done	(35355)
37	done	(33457)
36	done	(30998)
35	done	(30151)
34	done	(27816)
33	done	(25715)
32	done	(24412)
31	done	(22316)
30	done	(20972)
29	done	(19123)

40146239	Sequences
310358	Tags rejected (0.8%) at 27.0% coverage cutoff (0.010000 FDR).


	Elapsed time:
	   1154 seconds (900.72 CPU+SYS seconds)
[a5_s2] Building contigs from 8RS_CAGATC_L005_outputFile_A5.ec.fastq with IDBA
[a5_s2] Building contigs from 8RS_CAGATC_L005_outputFile_A5.ec.fastq with IDBA
[a5] idba -r 8RS_CAGATC_L005_outputFile_A5.s2/8RS_CAGATC_L005_outputFile_A5.ec.fasta -o 8RS_CAGATC_L005_outputFile_A5.s2/8RS_CAGATC_L005_outputFile_A5 --mink 29 --maxk 90
Message: after addback total kmer 65842289
Message: before operation: total kmer 65842289 edges 65550683
Message: tangle 540238 total 1074370
Message: trim 187448 dead ends
Message: tangle 357100 total 859171
Message: trim 109771 dead ends
Message: tangle 250442 total 740219
Message: trim 148226 dead ends
Message: tangle 105731 total 587680
Message: trim 66061 dead ends
Message: tangle 43024 total 519011
Message: remove 202178 low coverage contigs (< 7.7273)
Message: total kmer 19203419
Message: tangle 15800 total 164580
Message: start iteration from mink = 29 to maxk = 90
Message: k = 29, remove 10923 dead end, 70 stand alone, remain 148770 branches
Message: k = 30, remove 2692 dead end, 8 stand alone, remain 143674 branches
Message: k = 31, remove 2356 dead end, 7 stand alone, remain 142353 branches
Message: k = 32, remove 1339 dead end, 3 stand alone, remain 141130 branches
Message: k = 33, remove 1501 dead end, 8 stand alone, remain 137066 branches
Message: k = 34, remove 1398 dead end, 3 stand alone, remain 136768 branches
Message: k = 35, remove 1214 dead end, 1 stand alone, remain 135471 branches
Message: k = 36, remove 1385 dead end, 8 stand alone, remain 131602 branches
Message: k = 37, remove 1325 dead end, 2 stand alone, remain 130957 branches
Message: k = 38, remove 1327 dead end, 2 stand alone, remain 129841 branches
Message: k = 39, remove 1581 dead end, 3 stand alone, remain 126338 branches
Message: k = 40, remove 1501 dead end, 3 stand alone, remain 125759 branches
Message: k = 41, remove 1549 dead end, 3 stand alone, remain 124199 branches
Message: k = 42, remove 1692 dead end, 3 stand alone, remain 121100 branches
Message: k = 43, remove 1590 dead end, 1 stand alone, remain 120042 branches
Message: k = 44, remove 1518 dead end, 2 stand alone, remain 118376 branches
Message: k = 45, remove 1619 dead end, 3 stand alone, remain 115338 branches
Message: k = 46, remove 1609 dead end, 5 stand alone, remain 114234 branches
Message: k = 47, remove 1619 dead end, 1 stand alone, remain 112818 branches
Message: k = 48, remove 1725 dead end, 2 stand alone, remain 109802 branches
Message: k = 49, remove 1691 dead end, 4 stand alone, remain 108372 branches
Message: k = 50, remove 1659 dead end, 1 stand alone, remain 106869 branches
Message: k = 51, remove 1762 dead end, 2 stand alone, remain 103926 branches
Message: k = 52, remove 1652 dead end, 1 stand alone, remain 102705 branches
Message: k = 53, remove 1631 dead end, 3 stand alone, remain 100910 branches
Message: k = 54, remove 1724 dead end, 4 stand alone, remain 98227 branches
Message: k = 55, remove 1662 dead end, 0 stand alone, remain 96874 branches
Message: k = 56, remove 1688 dead end, 0 stand alone, remain 94958 branches
Message: k = 57, remove 1737 dead end, 4 stand alone, remain 92432 branches
Message: k = 58, remove 1702 dead end, 5 stand alone, remain 90899 branches
Message: k = 59, remove 1627 dead end, 5 stand alone, remain 89154 branches
Message: k = 60, remove 1642 dead end, 4 stand alone, remain 86521 branches
Message: k = 61, remove 1533 dead end, 1 stand alone, remain 85129 branches
Message: k = 62, remove 1567 dead end, 5 stand alone, remain 83428 branches
Message: k = 63, remove 1606 dead end, 1 stand alone, remain 81232 branches
Message: k = 64, remove 1559 dead end, 7 stand alone, remain 79758 branches
Message: k = 65, remove 1520 dead end, 0 stand alone, remain 78085 branches
Message: k = 66, remove 1584 dead end, 4 stand alone, remain 76001 branches
Message: k = 67, remove 1501 dead end, 4 stand alone, remain 74488 branches
Message: k = 68, remove 1508 dead end, 3 stand alone, remain 72938 branches
Message: k = 69, remove 1499 dead end, 6 stand alone, remain 70945 branches
Message: k = 70, remove 1470 dead end, 10 stand alone, remain 69443 branches
Message: k = 71, remove 1433 dead end, 8 stand alone, remain 67796 branches
Message: k = 72, remove 1473 dead end, 6 stand alone, remain 65723 branches
Message: k = 73, remove 1346 dead end, 4 stand alone, remain 64336 branches
Message: k = 74, remove 1332 dead end, 6 stand alone, remain 62855 branches
Message: k = 75, remove 1336 dead end, 10 stand alone, remain 61059 branches
Message: k = 76, remove 1249 dead end, 4 stand alone, remain 59732 branches
Message: k = 77, remove 1242 dead end, 6 stand alone, remain 58290 branches
Message: k = 78, remove 1308 dead end, 2 stand alone, remain 56500 branches
Message: k = 79, remove 1333 dead end, 4 stand alone, remain 55109 branches
Message: k = 80, remove 1271 dead end, 4 stand alone, remain 53685 branches
Message: k = 81, remove 1204 dead end, 8 stand alone, remain 51963 branches
Message: k = 82, remove 1176 dead end, 5 stand alone, remain 50646 branches
Message: k = 83, remove 1120 dead end, 8 stand alone, remain 49359 branches
Message: k = 84, remove 1048 dead end, 10 stand alone, remain 47868 branches
Message: k = 85, remove 961 dead end, 5 stand alone, remain 46865 branches
Message: k = 86, remove 943 dead end, 5 stand alone, remain 45677 branches
Message: k = 87, remove 866 dead end, 7 stand alone, remain 44482 branches
Message: k = 88, remove 842 dead end, 7 stand alone, remain 43557 branches
Message: k = 89, remove 776 dead end, 10 stand alone, remain 42614 branches
Message: remove 3948 bubbles
Message: k = 90, remove 739 dead end, 3 stand alone, remain 29690 branches
[a5] Preprocess libraries for scaffolding with SSPACE
[a5] Making initial estimates of insert size
[bwa_index] Pack FASTA... 0.37 sec
[bwa_index] Reverse the packed sequence... 0.10 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 5.62 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 5.32 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Update reverse BWT... 0.07 sec
[bwa_index] Construct SA from BWT and Occ... 1.54 sec
[bwa_index] Construct SA from reverse BWT and Occ... 1.41 sec
[a5] Using 40000 read pairs for mapping
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 4.42 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 40000 sequences have been processed.
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 4.07 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 40000 sequences have been processed.
[a5] java -jar GetInsertSize.jar 8RS_CAGATC_L005_outputFile_A5.raw1.sub.pe.sam
[a5_ise] Getting insert stats for /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/8RS_CAGATC_L005_outputFile_A5.raw1.sub.pe.sam
[a5] Will merge libraries if similar enough
[a5] aggregating libraries. n = 1
[bwa_index] Pack FASTA... 0.32 sec
[bwa_index] Reverse the packed sequence... 0.09 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 5.58 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 5.32 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Update reverse BWT... 0.06 sec
[bwa_index] Construct SA from BWT and Occ... 1.54 sec
[bwa_index] Construct SA from reverse BWT and Occ... 1.35 sec
[a5] Using 40000 read pairs for mapping
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 4.20 sec
[bwa_aln_core] write to the disk... 0.00 sec
[bwa_aln_core] 40000 sequences have been processed.
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 4.25 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 40000 sequences have been processed.
[a5] java -jar GetInsertSize.jar 8RS_CAGATC_L005_outputFile_A5.raw1.sub.pe.sam
[a5_ise] Getting insert stats for /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/8RS_CAGATC_L005_outputFile_A5.raw1.sub.pe.sam
[a5] Printing preprocessed library file to 8RS_CAGATC_L005_outputFile_A5.preproc.libs
[a5] Processed libraries:
     raw1:
      id=raw1
      p1=8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.pp.ec.fastq
      p2=8RS_CAGATC_L005_R2_illuminaformat_sed.fastq.pp.ec.fastq
      rc=0
      ins=302
      err=0.656
      nlibs=1
      libfile=8RS_CAGATC_L005_outputFile_A5.library_1.txt
[a5_s3] Scaffolding contigs from 8RS_CAGATC_L005_outputFile_A5.contigs.fasta with SSPACE
[a5] Total contig length 19806217
[a5] raw1: Insert 302, coverage 5.38, expected links 16
[a5] SSPACE -m 28 -n 11 -k 1 -a 0.4 -o 1 -x 0 -l 8RS_CAGATC_L005_outputFile_A5.library_1.txt -s 8RS_CAGATC_L005_outputFile_A5.contigs.fasta -b 8RS_CAGATC_L005_outputFile_A5.raw1 -d 8RS_CAGATC_L005_outputFile_A5.s3 > 8RS_CAGATC_L005_outputFile_A5.s3/8RS_CAGATC_L005_outputFile_A5.raw1.out
[a5_s3] Scaffolding contigs from 8RS_CAGATC_L005_outputFile_A5.contigs.fasta with SSPACE
[a5_s4] Detecting and breaking misassemblies in 8RS_CAGATC_L005_outputFile_A5.crude.scaffolds.fasta with A5QC
[a5] Identifying misassemblies in 8RS_CAGATC_L005_outputFile_A5.crude.scaffolds.fasta with 8RS_CAGATC_L005_outputFile_A5.qc.libraw1
[a5_s4] Detecting and breaking misassemblies in 8RS_CAGATC_L005_outputFile_A5.crude.scaffolds.fasta with A5QC
[bwa_index] Pack FASTA... 0.36 sec
[bwa_index] Reverse the packed sequence... 0.11 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 5.68 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 5.45 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Update reverse BWT... 0.07 sec
[bwa_index] Construct SA from BWT and Occ... 1.41 sec
[bwa_index] Construct SA from reverse BWT and Occ... 1.37 sec
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 25.05 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 25.06 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.96 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.91 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.79 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.85 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.86 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 24.13 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 2090830 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.75 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.74 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.76 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.74 sec
[bwa_aln_core] refine gapped alignments... 0.32 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.73 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.91 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.76 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.74 sec
[bwa_aln_core] refine gapped alignments... 0.31 sec
[bwa_aln_core] print alignments... 0.92 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] convert to sequence coordinate... 0.71 sec
[bwa_aln_core] refine gapped alignments... 0.30 sec
[bwa_aln_core] print alignments... 0.90 sec
[bwa_aln_core] 2090830 sequences have been processed.
[samopen] SAM header is present: 9589 sequences.
[bam_sort_core] merging from 2 files...
[a5] java -Xmx10589m -jar A5qc.jar 8RS_CAGATC_L005_outputFile_A5.s4/8RS_CAGATC_L005_outputFile_A5.qc.libraw1.sam 8RS_CAGATC_L005_outputFile_A5.crude.scaffolds.fasta 8RS_CAGATC_L005_outputFile_A5.s4/8RS_CAGATC_L005_outputFile_A5.qc.libraw1.broken.fasta 1 > 8RS_CAGATC_L005_outputFile_A5.s4/8RS_CAGATC_L005_outputFile_A5.qc.libraw1.qc.out
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/bwa index 8RS_CAGATC_L005_outputFile_A5.final.scaffolds.fasta
[a5_s5] No misassemblies found.
[bwa_index] Pack FASTA... 0.22 sec
[bwa_index] Reverse the packed sequence... 0.07 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 5.76 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 5.31 seconds elapse.
[bwa_index] Update BWT... 0.07 sec
[bwa_index] Update reverse BWT... 0.07 sec
[bwa_index] Construct SA from BWT and Occ... 1.40 sec
[bwa_index] Construct SA from reverse BWT and Occ... 1.37 sec
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/bwa aln 8RS_CAGATC_L005_outputFile_A5.final.scaffolds.fasta 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.pp.ec.fastq > 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.pp.ec.fastq.sai
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 21.88 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.87 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.84 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.50 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 1045415 sequences have been processed.
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/bwa aln 8RS_CAGATC_L005_outputFile_A5.final.scaffolds.fasta 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq.pp.ec.fastq > 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq.pp.ec.fastq.sai
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 21.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.76 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.78 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 21.39 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 1045415 sequences have been processed.
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/bwa sampe 8RS_CAGATC_L005_outputFile_A5.final.scaffolds.fasta 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.pp.ec.fastq.sai 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq.pp.ec.fastq.sai 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.pp.ec.fastq 8RS_CAGATC_L005_R2_illuminaformat_sed.fastq.pp.ec.fastq | /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/samtools view -b -S - | /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/samtools sort - raw1.pe
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (300, 312, 326)
[infer_isize] low and high boundaries: 248 and 378 for estimating avg and std
[infer_isize] inferred external isize from 136967 pairs: 309.802 +/- 17.995
[infer_isize] skewness: -0.087; kurtosis: 1.292; ap_prior: 5.56e-04
[infer_isize] inferred maximum insert size: 422 (6.25 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.21 sec
[bwa_sai2sam_pe_core] changing coordinates of 12365 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9616 out of 16627 Q17 singletons are mated.
[bwa_paired_sw] 8738 out of 48019 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 29.28 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.55 sec
[bwa_sai2sam_pe_core] print alignments... [samopen] SAM header is present: 9589 sequences.
3.37 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (300, 312, 327)
[infer_isize] low and high boundaries: 246 and 381 for estimating avg and std
[infer_isize] inferred external isize from 137524 pairs: 309.891 +/- 18.490
[infer_isize] skewness: -0.022; kurtosis: 1.610; ap_prior: 5.11e-04
[infer_isize] inferred maximum insert size: 425 (6.25 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.67 sec
[bwa_sai2sam_pe_core] changing coordinates of 12375 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9537 out of 16511 Q17 singletons are mated.
[bwa_paired_sw] 8962 out of 47141 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 32.81 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.61 sec
[bwa_sai2sam_pe_core] print alignments... 3.34 sec
[bwa_sai2sam_pe_core] 524288 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (300, 312, 327)
[infer_isize] low and high boundaries: 246 and 381 for estimating avg and std
[infer_isize] inferred external isize from 138111 pairs: 309.957 +/- 18.529
[infer_isize] skewness: -0.036; kurtosis: 1.595; ap_prior: 4.94e-04
[infer_isize] inferred maximum insert size: 426 (6.25 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.67 sec
[bwa_sai2sam_pe_core] changing coordinates of 12572 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9381 out of 16158 Q17 singletons are mated.
[bwa_paired_sw] 8909 out of 46645 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 32.54 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.61 sec
[bwa_sai2sam_pe_core] print alignments... 3.35 sec
[bwa_sai2sam_pe_core] 786432 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate... 
[infer_isize] (25, 50, 75) percentile: (300, 312, 326)
[infer_isize] low and high boundaries: 248 and 378 for estimating avg and std
[infer_isize] inferred external isize from 135151 pairs: 309.801 +/- 18.033
[infer_isize] skewness: -0.064; kurtosis: 1.366; ap_prior: 5.42e-04
[infer_isize] inferred maximum insert size: 423 (6.25 sigma)
[bwa_sai2sam_pe_core] time elapses: 3.65 sec
[bwa_sai2sam_pe_core] changing coordinates of 12253 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 9357 out of 16167 Q17 singletons are mated.
[bwa_paired_sw] 8332 out of 47278 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 32.59 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.61 sec
[bwa_sai2sam_pe_core] print alignments... 3.31 sec
[bwa_sai2sam_pe_core] 1045415 sequences have been processed.
[bam_sort_core] merging from 2 files...
[a5] /share/scratch/z3321306/ngopt_a5pipeline_linux-x64/bin/samtools index raw1.pe.bam
[a5] Final assembly in 8RS_CAGATC_L005_outputFile_A5.final.scaffolds.fasta
