[a5] Found the following libraries:
     raw1:
      id=raw1
      p1=8RS_CAGATC_L005_R1_illuminaformat_sed.fastq
      p2=8RS_CAGATC_L005_R2_illumina_sed.fastq
[a5] Cleaning reads with SGA
148311540
[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_illumina_sed.fastq


Preprocess stats:
Reads parsed:	78419520
Reads kept:	76926345 (0.980959)
Reads failed primer screen:	355526 (0.00453364)
Bases parsed:	7920371520
Bases kept:	7308158473 (0.922704)
Number of incorrectly paired reads that were discarded: 0
[timer - sga preprocess] wall clock: 436.12s CPU: 423.61s
[a5] sga index -d 74155770 -t 4 8RS_A5_pipeline.s1/8RS_A5_pipeline.pp.fastq > 8RS_A5_pipeline.s1/index.out 2> 8RS_A5_pipeline.s1/index.err
[a5] sga correct -t 4 -o 8RS_A5_pipeline.s1/8RS_A5_pipeline.pp.ec.fa 8RS_A5_pipeline.s1/8RS_A5_pipeline.pp.fastq > 8RS_A5_pipeline.s1/correct.out
[timer - sga::correct] wall clock: 10541.67s CPU: 40685.01s
Use of uninitialized value in concatenation (.) or string at ./bin/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 ./bin/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_illumina_sed.fastq
[a5] /home/bgansw/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_illumina_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_illumina_sed.fastq

Preprocess stats:
Reads parsed:	78419520
Reads kept:	75523268 (0.963067)
Reads failed primer screen:	355526 (0.00453364)
Bases parsed:	7920371520
Bases kept:	7195452685 (0.908474)
Number of incorrectly paired reads that were discarded: 0
[timer - sga preprocess] wall clock: 282.27s CPU: 280.96s
[a5] /home/bgansw/ngopt_a5pipeline_linux-x64/bin/sga correct -t 4 -p 8RS_A5_pipeline.pp -o 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp.ec.fastq 8RS_CAGATC_L005_R1_illuminaformat_sed.fastq.both.pp > 8RS_A5_pipeline.s1/raw1.correct.out
Warning, FASTQ quality string is not the same length as the sequence string for read @HWI-ST705:113:C026NACXX:5:1208:5169:188022/2
[timer - sga::correct] wall clock: 3335.27s CPU: 12868.67s
[a5] /home/bgansw/ngopt_a5pipeline_linux-x64/bin/tagdust -s /home/bgansw/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

0	Sequences
0	Tags rejected (-nan%) at 100.0% coverage cutoff (0.010000 FDR).


	Elapsed time:
	        seconds (0.00 CPU+SYS seconds)
[a5] tagdust -s -o 8RS_A5_pipeline.s1/8RS_A5_pipeline.dusted.fq /home/bgansw/ngopt_a5pipeline_linux-x64/bin/../adapter.fasta 8RS_A5_pipeline.s1/8RS_A5_pipeline.pp.ec.fa
TagDust version 1.13, Copyright (C) 2009 Timo Lassmann <timolassmann@gmail.com>
Creating Library
Generating Background
101	done	(53332821)
100	done	(1027489)
99	done	(1270842)
98	done	(1393773)
97	done	(1308139)
96	done	(1170701)
95	done	(1066323)
94	done	(952865)
93	done	(810710)
92	done	(720385)
91	done	(661173)
90	done	(603243)
89	done	(562373)
88	done	(520824)
87	done	(487244)
86	done	(459038)
85	done	(436218)
84	done	(418815)
83	done	(393875)
82	done	(376637)
81	done	(362309)
80	done	(338306)
79	done	(321161)
78	done	(298170)
77	done	(274432)
76	done	(257098)
75	done	(314474)
74	done	(301642)
73	done	(287548)
72	done	(273911)
71	done	(263320)
70	done	(249772)
69	done	(240136)
68	done	(229278)
67	done	(219431)
66	done	(209157)
65	done	(202303)
64	done	(194594)
63	done	(190823)
62	done	(184640)
61	done	(177603)
60	done	(170937)
59	done	(168655)
58	done	(161622)
57	done	(159178)
56	done	(150866)
55	done	(142609)
54	done	(134179)
53	done	(127274)
52	done	(117931)
51	done	(107099)
50	done	(133760)
49	done	(128496)
48	done	(126274)
47	done	(122676)
46	done	(119622)
45	done	(114627)
44	done	(111710)
43	done	(107818)
42	done	(103922)
41	done	(101400)
40	done	(97662)
39	done	(95009)
38	done	(92852)
37	done	(90837)
36	done	(85361)
35	done	(81425)
34	done	(76801)
33	done	(73348)
32	done	(70711)
31	done	(65628)
30	done	(62790)
29	done	(59669)

76926344	Sequences
772727	Tags rejected (1.0%) at 26.0% coverage cutoff (0.010000 FDR).


	Elapsed time:
	   1188 seconds (1187.40 CPU+SYS seconds)
[a5_s2] Building contigs from 8RS_A5_pipeline.ec.fastq with IDBA
[a5_s2] Building contigs from 8RS_A5_pipeline.ec.fastq with IDBA
[a5] idba -r 8RS_A5_pipeline.s2/8RS_A5_pipeline.ec.fasta -o 8RS_A5_pipeline.s2/8RS_A5_pipeline --mink 29 --maxk 90
Message: after addback total kmer 46684461
Message: before operation: total kmer 46684461 edges 46531343
Message: tangle 373539 total 839620
Message: trim 139276 dead ends
Message: tangle 240008 total 662356
Message: trim 74460 dead ends
Message: tangle 168206 total 578483
Message: trim 95506 dead ends
Message: tangle 75813 total 479721
Message: trim 41386 dead ends
Message: tangle 37795 total 436358
Message: remove 170885 low coverage contigs (< 6.4609)
Message: total kmer 14351695
Message: tangle 15696 total 121943
Message: start iteration from mink = 29 to maxk = 90
Message: k = 29, remove 8566 dead end, 155 stand alone, remain 110116 branches
Message: k = 30, remove 2762 dead end, 32 stand alone, remain 107075 branches
Message: k = 31, remove 2463 dead end, 24 stand alone, remain 105031 branches
Message: k = 32, remove 1248 dead end, 5 stand alone, remain 103445 branches
Message: k = 33, remove 1344 dead end, 6 stand alone, remain 100872 branches
Message: k = 34, remove 1195 dead end, 3 stand alone, remain 100140 branches
Message: k = 35, remove 982 dead end, 3 stand alone, remain 98885 branches
Message: k = 36, remove 1082 dead end, 6 stand alone, remain 96355 branches
Message: k = 37, remove 933 dead end, 5 stand alone, remain 95613 branches
Message: k = 38, remove 904 dead end, 0 stand alone, remain 94522 branches
Message: k = 39, remove 1133 dead end, 3 stand alone, remain 92246 branches
Message: k = 40, remove 1032 dead end, 3 stand alone, remain 91468 branches
Message: k = 41, remove 1037 dead end, 1 stand alone, remain 90057 branches
Message: k = 42, remove 1119 dead end, 1 stand alone, remain 88090 branches
Message: k = 43, remove 1049 dead end, 4 stand alone, remain 87222 branches
Message: k = 44, remove 1031 dead end, 2 stand alone, remain 85846 branches
Message: k = 45, remove 1074 dead end, 3 stand alone, remain 83834 branches
Message: k = 46, remove 1037 dead end, 1 stand alone, remain 82964 branches
Message: k = 47, remove 1028 dead end, 5 stand alone, remain 81775 branches
Message: k = 48, remove 1032 dead end, 1 stand alone, remain 79881 branches
Message: k = 49, remove 967 dead end, 4 stand alone, remain 78840 branches
Message: k = 50, remove 938 dead end, 4 stand alone, remain 77746 branches
Message: k = 51, remove 937 dead end, 6 stand alone, remain 75892 branches
Message: k = 52, remove 878 dead end, 3 stand alone, remain 75085 branches
Message: k = 53, remove 880 dead end, 0 stand alone, remain 73958 branches
Message: k = 54, remove 879 dead end, 0 stand alone, remain 72431 branches
Message: k = 55, remove 876 dead end, 2 stand alone, remain 71543 branches
Message: k = 56, remove 866 dead end, 0 stand alone, remain 70342 branches
Message: k = 57, remove 927 dead end, 6 stand alone, remain 68911 branches
Message: k = 58, remove 917 dead end, 2 stand alone, remain 67934 branches
Message: k = 59, remove 904 dead end, 0 stand alone, remain 66755 branches
Message: k = 60, remove 889 dead end, 3 stand alone, remain 65179 branches
Message: k = 61, remove 792 dead end, 0 stand alone, remain 64304 branches
Message: k = 62, remove 757 dead end, 1 stand alone, remain 63320 branches
Message: k = 63, remove 797 dead end, 4 stand alone, remain 61967 branches
Message: k = 64, remove 793 dead end, 1 stand alone, remain 61023 branches
Message: k = 65, remove 804 dead end, 1 stand alone, remain 59985 branches
Message: k = 66, remove 817 dead end, 2 stand alone, remain 58764 branches
Message: k = 67, remove 795 dead end, 4 stand alone, remain 57708 branches
Message: k = 68, remove 728 dead end, 3 stand alone, remain 56796 branches
Message: k = 69, remove 751 dead end, 1 stand alone, remain 55662 branches
Message: k = 70, remove 759 dead end, 2 stand alone, remain 54771 branches
Message: k = 71, remove 691 dead end, 1 stand alone, remain 53801 branches
Message: k = 72, remove 685 dead end, 3 stand alone, remain 52594 branches
Message: k = 73, remove 639 dead end, 4 stand alone, remain 51830 branches
Message: k = 74, remove 633 dead end, 7 stand alone, remain 51047 branches
Message: k = 75, remove 618 dead end, 3 stand alone, remain 50025 branches
Message: k = 76, remove 612 dead end, 3 stand alone, remain 49274 branches
Message: k = 77, remove 567 dead end, 1 stand alone, remain 48516 branches
Message: k = 78, remove 584 dead end, 2 stand alone, remain 47407 branches
Message: k = 79, remove 595 dead end, 6 stand alone, remain 46662 branches
Message: k = 80, remove 581 dead end, 4 stand alone, remain 45921 branches
Message: k = 81, remove 556 dead end, 3 stand alone, remain 44859 branches
Message: k = 82, remove 501 dead end, 2 stand alone, remain 44148 branches
Message: k = 83, remove 481 dead end, 2 stand alone, remain 43525 branches
Message: k = 84, remove 457 dead end, 4 stand alone, remain 42711 branches
Message: k = 85, remove 426 dead end, 5 stand alone, remain 42168 branches
Message: k = 86, remove 404 dead end, 1 stand alone, remain 41507 branches
Message: k = 87, remove 374 dead end, 2 stand alone, remain 40807 branches
Message: k = 88, remove 358 dead end, 2 stand alone, remain 40330 branches
Message: k = 89, remove 317 dead end, 5 stand alone, remain 39836 branches
Message: remove 3822 bubbles
Message: k = 90, remove 305 dead end, 0 stand alone, remain 27727 branches
[a5] Preprocess libraries for scaffolding with SSPACE
[a5] Making initial estimates of insert size
[bwa_index] Pack FASTA... 0.28 sec
[bwa_index] Reverse the packed sequence... 0.08 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 3.77 seconds elapse.
[bwa_index] Construct BWT for the reverse packed sequence...
[bwa_index] 3.35 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Update reverse BWT... 0.05 sec
[bwa_index] Construct SA from BWT and Occ... 0.72 sec
[bwa_index] Construct SA from reverse BWT and Occ... 0.71 sec
[a5] Found only 0 read pairs in library
[a5] Using 0 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] 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
[a5] java -jar GetInsertSize.jar 8RS_A5_pipeline.raw1.sub.pe.sam
[a5_ise] Getting insert stats for /home/bgansw/ngopt_a5pipeline_linux-x64/8RS_A5_pipeline.raw1.sub.pe.sam
Exception in thread "main" java.lang.ClassFormatError: org.halophiles.assembly.SAMFileParser (unrecognized class file version)
   at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
   at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
   at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
   at java.net.URLClassLoader.findClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at org.halophiles.assembly.InsertSizeExporter.main(InsertSizeExporter.java:36)
Use of uninitialized value in numeric gt (>) at ./bin/a5_pipeline.pl line 1205, <IN> line 55454.
Use of uninitialized value in concatenation (.) or string at ./bin/a5_pipeline.pl line 1211, <IN> line 55454.
[a5] Discarding estimate. Not enough data points: 
Use of uninitialized value in multiplication (*) at ./bin/a5_pipeline.pl line 1212, <IN> line 55454.
[a5_preproc] Insert estimate for raw1 not reliable.[a5_preproc] No insert estimate for raw1. Please provide one in a library file. Exiting