Version 2.04: released on July 13th, 2012
Compile Jan 27 2015     11:50:30

********************
Pregraph
********************

Parameters: pregraph -s /data/idiv_schielzeth/Grasshoppers/Gsib_Green_Brown_HiSeqX_libs_2018/F18FTSEUHT0360_G.SbluR/raw_reads/G.sibiricusGreen/assembly/Gsib_GB_final_assembly/config_G.sibGB_half_paired.txt -K 43 -p 16 -R -o assembly_G.sibGB_half_assembly3

In /data/idiv_schielzeth/Grasshoppers/Gsib_Green_Brown_HiSeqX_libs_2018/F18FTSEUHT0360_G.SbluR/raw_reads/G.sibiricusGreen/assembly/Gsib_GB_final_assembly/config_G.sibGB_half_paired.txt, 1 lib(s), maximum read length 150, maximum name length 256.

16 thread(s) initialized.
Import reads from file:
 /data/idiv_schielzeth/Grasshoppers/Bielefeld/Gsib_GB_HiSeqX_final_satminer_run/subsampled/Gsib_GB_R1_half_sample.fastq
Import reads from file:
 /data/idiv_schielzeth/Grasshoppers/Bielefeld/Gsib_GB_HiSeqX_final_satminer_run/subsampled/Gsib_GB_R2_half_sample.fastq
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.

#maximal read length
max_rd_len=150
[LIB]
#average insert size
avg_ins=250
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=150
#in which order the reads are used while scaffolding
rank=1
#cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=/data/idiv_schielzeth/Grasshoppers/Bielefeld/Gsib_GB_HiSeqX_final_satminer_run/subsampled/Gsib_GB_R1_half_sample.fastq
q2=/data/idiv_schielzeth/Grasshoppers/Bielefeld/Gsib_GB_HiSeqX_final_satminer_run/subsampled/Gsib_GB_R2_half_sample.fastq

pregraph_sparse_63mer.v1.0.3 cleaning done.
pregraph_sparse_63mer.v1.0.3 objects generated.
SOAPdenovo-63mer cleaning done.
SOAPdenovo-63mer objects generated.
sparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*) [clone .constprop.58]':
io_func.cpp:(.text+0x47): undefined reference to `samread'
io_func.cpp:(.text+0xe2): undefined reference to `bam_format1_core'
sparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*)':
io_func.cpp:(.text+0x66a): undefined reference to `samread'
io_func.cpp:(.text+0x70a): undefined reference to `bam_format1_core'
standardPregraph/readseq1by1.o: In function `read1seqbam':
readseq1by1.c:(.text+0xac7): undefined reference to `samread'
readseq1by1.c:(.text+0xaec): undefined reference to `bam_format1_core'
./sparsePregraph/inc/libbam.a(sam.o): In function `samthreads':
/home/yisoo/samtools-1.9/sam.c:35: undefined reference to `hts_get_format'
/home/yisoo/samtools-1.9/sam.c:36: undefined reference to `bgzf_mt'
./sparsePregraph/inc/libbam.a(sam.o): In function `samopen':
/home/yisoo/samtools-1.9/sam.c:43: undefined reference to `hts_open'
/home/yisoo/samtools-1.9/sam.c:55: undefined reference to `hts_set_fai_filename'
/home/yisoo/samtools-1.9/sam.c:61: undefined reference to `sam_hdr_read'
/home/yisoo/samtools-1.9/sam.c:68: undefined reference to `hts_verbose'
/home/yisoo/samtools-1.9/sam.c:72: undefined reference to `hts_get_format'
/home/yisoo/samtools-1.9/sam.c:76: undefined reference to `sam_hdr_write'
/home/yisoo/samtools-1.9/sam.c:77: undefined reference to `hts_verbose'
/home/yisoo/samtools-1.9/sam.c:79: undefined reference to `hts_close'
/home/yisoo/samtools-1.9/sam.c:48: undefined reference to `hts_close'
./sparsePregraph/inc/libbam.a(sam.o): In function `samclose':
/home/yisoo/samtools-1.9/sam.c:92: undefined reference to `bam_hdr_destroy'
/home/yisoo/samtools-1.9/sam.c:93: undefined reference to `hts_close'
./sparsePregraph/inc/libbam.a(sam.o): In function `samfetch':
/home/yisoo/samtools-1.9/sam.c:100: undefined reference to `bam_init1'
/home/yisoo/samtools-1.9/sam.c:101: undefined reference to `sam_itr_queryi'
/home/yisoo/samtools-1.9/sam.c:103: undefined reference to `hts_itr_next'
/home/yisoo/samtools-1.9/sam.c:104: undefined reference to `hts_itr_destroy'
/home/yisoo/samtools-1.9/sam.c:105: undefined reference to `bam_destroy1'
./sparsePregraph/inc/libbam.a(sam.o): In function `sampileup':
/home/yisoo/samtools-1.9/sam.c:114: undefined reference to `bam_init1'
./sparsePregraph/inc/libbam.a(sam.o): In function `samread':
/home/yisoo/samtools-1.9/sam.h:95: undefined reference to `sam_read1'
./sparsePregraph/inc/libbam.a(sam.o): In function `sampileup':
/home/yisoo/samtools-1.9/sam.c:125: undefined reference to `bam_destroy1'
./sparsePregraph/inc/libbam.a(sam.o): In function `samfaipath':
/home/yisoo/samtools-1.9/sam.c:139: undefined reference to `hts_verbose'
/home/yisoo/samtools-1.9/sam.c:140: undefined reference to `fai_build'
./sparsePregraph/inc/libbam.a(bam_plbuf.o): In function `bam_plbuf_init':
/home/yisoo/samtools-1.9/bam_plbuf.c:47: undefined reference to `bam_plp_init'
./sparsePregraph/inc/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy':
/home/yisoo/samtools-1.9/bam_plbuf.c:55: undefined reference to `bam_plp_destroy'
./sparsePregraph/inc/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':
/home/yisoo/samtools-1.9/bam_plbuf.c:63: undefined reference to `bam_plp_push'
/home/yisoo/samtools-1.9/bam_plbuf.c:65: undefined reference to `bam_plp_next'
./sparsePregraph/inc/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset':
/home/yisoo/samtools-1.9/bam_plbuf.c:40: undefined reference to `bam_plp_reset'
collect2: error: ld returned 1 exit status
Makefile:56: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1

/usr/bin/X11/ld: final link failed: Symbol needs debug section which does not exist
collect2: error: ld returned 1 exit status
Makefile:65: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1

make[1]: Entering directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/sparsePregraph'
pregraph_sparse_63mer.v1.0.3 cleaning done.
multi_threads.cpp: In function 'void* threadRoutine(void*)':
multi_threads.cpp:93:3: error: 'usleep' was not declared in this scope
   usleep ( 1 );
   ^~~~~~
multi_threads.cpp:93:3: note: suggested alternative: 'fseek'
   usleep ( 1 );
   ^~~~~~
   fseek
multi_threads.cpp: In function 'void sendWorkSignal(unsigned char, unsigned char*)':
multi_threads.cpp:115:3: error: 'usleep' was not declared in this scope
   usleep ( 10 );
   ^~~~~~
multi_threads.cpp:115:3: note: suggested alternative: 'fseek'
   usleep ( 10 );
   ^~~~~~
   fseek
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc multi_threads.cpp
build_preArc.cpp: In function 'void build_preArc_threaded(preArc_array*, vertex_hash2*, int, int, std::vector<std::__cxx11::basic_string<char> >*, int)':
build_preArc.cpp:1071:28: error: 'usleep' was not declared in this scope
   while ( io_ready == 0 ) {usleep ( 1 );}
                            ^~~~~~
build_preArc.cpp:1071:28: note: suggested alternative: 'beep'
   while ( io_ready == 0 ) {usleep ( 1 );}
                            ^~~~~~
                            beep
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc build_preArc.cpp
pregraph_sparse.cpp: In function 'int call_pregraph_sparse(int, char**)':
pregraph_sparse.cpp:171:31: error: 'usleep' was not declared in this scope
      while ( io_ready == 0 ) {usleep ( 1 );}
                               ^~~~~~
pregraph_sparse.cpp:171:31: note: suggested alternative: 'fseek'
      while ( io_ready == 0 ) {usleep ( 1 );}
                               ^~~~~~
                               fseek
pregraph_sparse.cpp:284:31: error: 'usleep' was not declared in this scope
      while ( io_ready == 0 ) {usleep ( 1 );}
                               ^~~~~~
pregraph_sparse.cpp:284:31: note: suggested alternative: 'fseek'
      while ( io_ready == 0 ) {usleep ( 1 );}
                               ^~~~~~
                               fseek
pregraph_sparse.cpp: In function 'void initenv(int, char**)':
pregraph_sparse.cpp:504:2: error: 'optind' was not declared in this scope
  optind = 1;
  ^~~~~~
pregraph_sparse.cpp:504:2: note: suggested alternative: 'optarg'
  optind = 1;
  ^~~~~~
  optarg
pregraph_sparse.cpp:507:19: error: 'getopt' was not declared in this scope
  while ( ( copt = getopt ( argc, argv, "s:o:K:g:z:d:e:p:m:r:R" ) ) != EOF )
                   ^~~~~~
pregraph_sparse.cpp:507:19: note: suggested alternative: 'getpt'
  while ( ( copt = getopt ( argc, argv, "s:o:K:g:z:d:e:p:m:r:R" ) ) != EOF )
                   ^~~~~~
                   getpt
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc pregraph_sparse.cpp
make[1]: Leaving directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/sparsePregraph'
make[1]: Entering directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/standardPregraph'
SOAPdenovo-63mer cleaning done.
contig.c: In function 'call_heavygraph':
contig.c:78:2: warning: implicit declaration of function 'swapedge'; did you mean 'loadEdge'? [-Wimplicit-function-declaration]
  swapedge();
  ^~~~~~~~
  loadEdge
contig.c:79:2: warning: implicit declaration of function 'sortedge'; did you mean 'loadEdge'? [-Wimplicit-function-declaration]
  sortedge();
  ^~~~~~~~
  loadEdge
contig.c:80:2: warning: implicit declaration of function 'freshArc' [-Wimplicit-function-declaration]
  freshArc();
  ^~~~~~~~
contig.c:144:3: warning: implicit declaration of function 'Iterate' [-Wimplicit-function-declaration]
   Iterate ( shortrdsfile, graphfile, maxk, M ); //keepReadFile,
   ^~~~~~~
contig.c:154:3: warning: implicit declaration of function 'freshpreGraphBasic' [-Wimplicit-function-declaration]
   freshpreGraphBasic ( iter, maxk, graphfile );
   ^~~~~~~~~~~~~~~~~~
cutTipPreGraph.c: In function 'clipTipFromNode':
cutTipPreGraph.c:127:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
   PrintKmer ( stderr, word );
   ^~~~~~~~~
   print_kmer
hashFunction.c: In function 'crc32cHardware64':
hashFunction.c:111:9: warning: implicit declaration of function '__builtin_ia32_crc32di'; did you mean '__builtin_ia32_bsrdi'? [-Wimplicit-function-declaration]
   crc = __builtin_ia32_crc32di ( crc, * ( uint64_t * ) data );
         ^~~~~~~~~~~~~~~~~~~~~~
         __builtin_ia32_bsrdi
loadPreGraph.c: In function 'kmer2vt':
loadPreGraph.c:222:4: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
    PrintKmer ( stderr, kmer );
    ^~~~~~~~~
    print_kmer
localAsm.c: In function 'traceAlongDBgraph':
localAsm.c:657:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
   PrintKmer ( stderr, word );
   ^~~~~~~~~
   print_kmer
node2edge.c: In function 'merge_linearV2':
node2edge.c:505:5: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
     PrintKmer ( stderr, wordplus );
     ^~~~~~~~~
     print_kmer
orderContig.c: In function 'score_pass':
orderContig.c:2411:15: warning: implicit declaration of function 'allConnect'; did you mean 'validConnect'? [-Wimplicit-function-declaration]
  int outnum = allConnect ( id, NULL );
               ^~~~~~~~~~
               validConnect
output_pregraph.c: In function 'output_1edge':
output_pregraph.c:92:2: warning: implicit declaration of function 'print_kmer_gz'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
  print_kmer_gz ( fp, edge->from_node, ',' );
  ^~~~~~~~~~~~~
  print_kmer
prlRead2path.c: In function 'searchKmer':
prlRead2path.c:356:3: warning: implicit declaration of function 'PrintKmer'; did you mean 'print_kmer'? [-Wimplicit-function-declaration]
   PrintKmer ( stderr, kmerBuffer[t] );
   ^~~~~~~~~
   print_kmer
scaffold.c: In function 'call_scaffold':
scaffold.c:90:2: warning: implicit declaration of function 'ScafStat' [-Wimplicit-function-declaration]
  ScafStat ( 100, graphfile );
  ^~~~~~~~
cutTip_graph2.c: In function 'removeLowCovEdges2':
cutTip_graph2.c:231:2: warning: implicit declaration of function 'linearConcatenate2'; did you mean 'linearConcatenate'? [-Wimplicit-function-declaration]
  linearConcatenate2 ( last );
  ^~~~~~~~~~~~~~~~~~
  linearConcatenate
read2edge.c: In function 'Read2edge':
read2edge.c:960:19: warning: implicit declaration of function 'read1seqInLibpos'; did you mean 'read1seqInLib'? [-Wimplicit-function-declaration]
  while ( ( flag = read1seqInLibpos ( seqBuffer[read_c], next_name, & ( lenBuffer[read_c] ), //file,
                   ^~~~~~~~~~~~~~~~
                   read1seqInLib
iterate.c: In function 'update1Edge':
iterate.c:406:3: warning: implicit declaration of function 'destroyEdge2'; did you mean 'destroyArcMem'? [-Wimplicit-function-declaration]
   destroyEdge2 ( index );
   ^~~~~~~~~~~~
   destroyArcMem
iterate.c: In function 'addArc':
iterate.c:780:3: warning: implicit declaration of function 'Read2edge2'; did you mean 'prlRead2edge'? [-Wimplicit-function-declaration]
   Read2edge2 ( libfile, graph, last, maxk ); //, keepReadFile
   ^~~~~~~~~~
   prlRead2edge
iterate.c:783:5: warning: implicit declaration of function 'Read2edge'; did you mean 'prlRead2edge'? [-Wimplicit-function-declaration]
   { Read2edge ( libfile, graph, maxk ); }
     ^~~~~~~~~
     prlRead2edge
iterate.c:795:2: warning: implicit declaration of function 'removeDeadArcs2'; did you mean 'removeDeadArcs'? [-Wimplicit-function-declaration]
  removeDeadArcs2();
  ^~~~~~~~~~~~~~~
  removeDeadArcs
iterate.c: In function 'checkindegree':
iterate.c:1169:3: warning: implicit declaration of function 'arcCount2'; did you mean 'arcCount'? [-Wimplicit-function-declaration]
   arcCount2 ( from_ed, &arcRight_n );
   ^~~~~~~~~
   arcCount
iterate.c: In function 'swapedge':
iterate.c:1653:5: warning: implicit declaration of function 'copyEdge'; did you mean 'copy1Edge'? [-Wimplicit-function-declaration]
     copyEdge ( i, num_ed + 1 + 1 );
     ^~~~~~~~
     copy1Edge
iterate.c: In function 'Iterate':
iterate.c:2566:4: warning: implicit declaration of function 'removeWeakEdges2'; did you mean 'removeWeakEdges'? [-Wimplicit-function-declaration]
    removeWeakEdges2 ( cutlen, 1, mink );
    ^~~~~~~~~~~~~~~~
    removeWeakEdges
iterate.c:2567:4: warning: implicit declaration of function 'removeLowCovEdges2'; did you mean 'removeLowCovEdges'? [-Wimplicit-function-declaration]
    removeLowCovEdges2 ( cutlen, deLowEdge, mink, 0 );
    ^~~~~~~~~~~~~~~~~~
    removeLowCovEdges
iterate.c:2576:4: warning: implicit declaration of function 'cutTipsInGraph2'; did you mean 'cutTipsInGraph'? [-Wimplicit-function-declaration]
    cutTipsInGraph2 ( cutlen, 0, 0 );
    ^~~~~~~~~~~~~~~
    cutTipsInGraph
make[1]: Leaving directory '/panhome/bguinet/TOOLS/SOAPdenovo2-src-r240/standardPregraph'
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_import.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(sam.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_pileup.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(faidx.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(knetfile.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(sam_header.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bgzf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(kstring.o): relocation R_X86_64_32 against `.text' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(bam_aux.o): relocation R_X86_64_32S against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/X11/ld: ./sparsePregraph/inc/libbam.a(razf.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
standardPregraph/main.o: In function `main':
main.c:(.text.startup+0xee): undefined reference to `call_pregraph_sparse'
/usr/bin/X11/ld: final link failed: Symbol needs debug section which does not exist
collect2: error: ld returned 1 exit status
Makefile:65: recipe for target 'SOAPdenovo-63mer' failed
make: *** [SOAPdenovo-63mer] Error 1

In file included from build_graph.cpp:13:                 
./inc/global.h:30:10: fatal error: 'spinLock.h' file not found
#include "spinLock.h"

Version 2.04: released on July 13th, 2012
Compile Sep 16 2016     15:43:38
********************
Pregraph
********************
Parameters: pregraph -s bart_cfg_file -K 53 -p 20 -R -o bart_53 
In bart_cfg_file, 1 lib(s), maximum read length 120, maximum name length 256.
20 thread(s) initialized.
Import reads from file:
 /wing2/users/dcopetti/OGE_genomes_reads/new_datasets/bart_frag_SRR1528330_1.fastq
Import reads from file:
 /wing2/users/dcopetti/OGE_genomes_reads/new_datasets/bart_frag_SRR1528330_2.fastq
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.
--- 400000000th reads.

max_rd_len=120
[LIB]
#average insert size
avg_ins=400
#if sequence needs to be reversed
reverse_seq=0
asm_flags=3
rd_len_cutoff=120
rank=1
insert size)
pair_num_cutoff=3
least 32 for short insert size)
map_len=32
q1=/1.fastq
q2=/2.fastq

Parameters: pregraph_sparse -s soap2.config -K 21 -g 15 -z 5000000000 -d 1 -e 1 -R  -r 0 -p 4 -o ass_trim105_merged_k21

Start to build the sparse de Brujin graph, round: 1
1 io thread initialized.
Import reads from file:
 ../../../../merging/151117_trim105//MFS25ng/out.notCombined_1.fastq.gz
4 work threads initialized.
Import reads from file:
 ../../../../merging/151117_trim105//MFS25ng/out.notCombined_2.fastq.gz
Import reads from file:
 ../../../../merging/151117_trim105//MFS25ng/out.extendedFrags.fastq.gz
Command terminated by signal 11
    Command being timed: "/home/jov14/tools/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-127mer sparse_pregraph -z 5000000000 -o ass_trim105_merged_k21 -p 4 -s soap2.config -K 21 -d 1 -R"
    User time (seconds): 150.83
    System time (seconds): 24.50
    Percent of CPU this job got: 241%
    Elapsed (wall clock) time (h:mm:ss or m:ss): 1:12.63
    Average shared text size (kbytes): 0
    Average unshared data size (kbytes): 0
    Average stack size (kbytes): 0
    Average total size (kbytes): 0
    Maximum resident set size (kbytes): 6717512
    Average resident set size (kbytes): 0
    Major (requiring I/O) page faults: 0
    Minor (reclaiming a frame) page faults: 1210198
    Voluntary context switches: 222300
    Involuntary context switches: 6058
    Swaps: 0
    File system inputs: 0
    File system outputs: 13433984
    Socket messages sent: 0
    Socket messages received: 0
    Signals delivered: 0
    Page size (bytes): 4096
    Exit status: 0

********************
Scaff
********************

Parameters: scaff -g lithmul -F scaff: invalid option -- 'K'
-m

Files for scaffold construction are OK.

There are 1 grad(s), 629927998 read(s), max read len 150.
Kmer size: 117
There are 13429809 edge(s) in edge file.
Mask contigs with coverage lower than 2.2 or higher than 44.0, and strict length 0.
Average contig coverage is 22, 3187804 contig(s) masked.
Mask contigs shorter than 119, 524656 contig(s) masked.
17899968 arc(s) loaded, average weight is 10.
6714905 contig(s) loaded.
Done loading updated edges.
Time spent on loading updated edges: 60s.

*****************************************************
Start to load paired-end reads information.

Cannot open lithmul.readOnContig. Now exit to system...

cd ${rundir}

label=lithmul

${exedir}/SOAPdenovo-127mer sparse_pregraph -s ${rundir}/lithmul.config -K 117 -z 1700000000 -p 23 -o ${label}
${exedir}/SOAPdenovo-127mer contig -g ${label} -R -p 23 -K 117 -z 1700000000
${exedir}/SOAPdenovo-127mer map -s ${rundir}/lithmul.config -g ${label} -p 23 -K 117
${exedir}/SOAPdenovo-127mer scaff  -g ${label} -F -K 117 -z 1700000000

/finalFusion -K 33 -D -c /input/output.fa -g /output/soap
Mapping & Scaffolding module.
[main]Data prepare mode selected .
not enought memory

free -m
             total       used       free     shared    buffers     cached
Mem:        120984      94769      26214          0        106      86892
-/+ buffers/cache:       7770     113213
Swap:            0          0          0
vmstat -s
    123888000  total memory
     97044368  used memory
     64228880  active memory
     31563736  inactive memory
     26843632  free memory
       109368  buffer memory
     88977984  swap cache
            0  total swap
            0  used swap
            0  free swap
   9208005092 non-nice user cpu ticks
         8779 nice user cpu ticks
    367979891 system cpu ticks
   4830637734 idle cpu ticks
     21968833 IO-wait cpu ticks
        37217 IRQ cpu ticks
      5125532 softirq cpu ticks
       669352 stolen cpu ticks
     91741034 pages paged in
   1724763415 pages paged out
            0 pages swapped in
            0 pages swapped out
   2558299138 interrupts
   2576345523 CPU context switches
   1481842300 boot time
     79999921 forks

~/git/SOAPdenovo2 $ make

pregraph_sparse_63mer.v1.0.3 cleaning done.                         
pregraph_sparse_63mer.v1.0.3 objects generated.                    
SOAPdenovo-63mer cleaning done.                              
SOAPdenovo-63mer objects generated.                                
sparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*) [clone .constprop.58]':
io_func.cpp:(.text+0x47): undefined reference to `samread'
io_func.cpp:(.text+0xe2): undefined reference to `bam_format1_core'
sparsePregraph/io_func.o: In function `read1seqbam(char*, char*, int, samfile_t*, int*)':
io_func.cpp:(.text+0x62a): undefined reference to `samread'
io_func.cpp:(.text+0x6ca): undefined reference to `bam_format1_core'
standardPregraph/readseq1by1.o: In function `read1seqbam':
readseq1by1.c:(.text+0xaa7): undefined reference to `samread'
readseq1by1.c:(.text+0xacc): undefined reference to `bam_format1_core'
/lib64/libbam.a(sam.o): In function `samthreads':
(.text+0x11): undefined reference to `hts_get_format'
(.text+0x2c): undefined reference to `bgzf_mt'
/lib64/libbam.a(sam.o): In function `samopen':
(.text+0x62): undefined reference to `hts_open'
(.text+0xb8): undefined reference to `hts_set_fai_filename'
(.text+0xc9): undefined reference to `sam_hdr_read'
(.text+0xe6): undefined reference to `hts_verbose'
(.text+0x12d): undefined reference to `hts_get_format'
(.text+0x15f): undefined reference to `sam_hdr_write'
(.text+0x169): undefined reference to `hts_verbose'
(.text+0x195): undefined reference to `hts_close'
(.text+0x1c5): undefined reference to `hts_close'
/lib64/libbam.a(sam.o): In function `samclose':
(.text+0x1ea): undefined reference to `bam_hdr_destroy'
(.text+0x1f3): undefined reference to `hts_close'
/lib64/libbam.a(sam.o): In function `samfetch':
(.text+0x23a): undefined reference to `bam_init1'
(.text+0x255): undefined reference to `sam_itr_queryi'
(.text+0x279): undefined reference to `hts_itr_next'
(.text+0x28a): undefined reference to `hts_itr_destroy'
(.text+0x293): undefined reference to `bam_destroy1'
/lib64/libbam.a(sam.o): In function `sampileup':
(.text+0x2d6): undefined reference to `bam_init1'
(.text+0x333): undefined reference to `sam_read1'
(.text+0x354): undefined reference to `bam_destroy1'
/lib64/libbam.a(sam.o): In function `samfaipath':
(.text+0x3ed): undefined reference to `hts_verbose'
(.text+0x3f9): undefined reference to `fai_build'
/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset':
(.text+0x5): undefined reference to `bam_plp_reset'
/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_init':
(.text+0x33): undefined reference to `bam_plp_init'
/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy':
(.text+0x59): undefined reference to `bam_plp_destroy'
/lib64/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':
(.text+0x95): undefined reference to `bam_plp_push'
(.text+0xd4): undefined reference to `bam_plp_next'
collect2: error: ld returned 1 exit status
make: *** [Makefile:58: SOAPdenovo-63mer] Error 1

~/git/SOAPdenovo2 $ make -v

GNU Make 4.2.1
Built for x86_64-unknown-linux-gnu

Version 2.04: released on July 13th, 2012
Compile Sep 25 2015     11:07:28

********************
Pregraph
********************

Parameters: pregraph -s test.cfg -K 41 -p 30 -R -o test_K41 

In test.cfg, 1 lib(s), maximum read length 600, maximum name length 256.

30 thread(s) initialized.
Import reads from file:
 /data/archive/YL-GF-02/trimmed/2011WAN043/trim_pe1.fastq.gz
Import reads from file:
 /data/archive/YL-GF-02/trimmed/2011WAN043/trim_pe2.fastq.gz
Import reads from file:
 /data/archive/YL-GF-02/trimmed/2011WAN043/trim_sing1.fastq.gz
Import reads from file:
 /data/archive/YL-GF-02/trimmed/2011WAN043/trim_sing2.fastq.gz
Time spent on hashing reads: 676s, 89689873 read(s) processed.
LIB(s) information:
 [LIB] 0, avg_ins 317, reverse 0.
854464360 node(s) allocated, 5137311711 kmer(s) in reads, 5137311711 kmer(s) processed.
done hashing nodes
828819958 linear node(s) marked.
Time spent on marking linear nodes: 15s.
Time spent on pre-graph construction: 691s.

Start to remove frequency-one-kmer tips shorter than 82.
Kmer 0 0 2d199 b575fb763403b451 is not found, node1 0 0 34666 d5d7edd8d00ed145 .

/software/megahit_v1.1.1_LINUX_CPUONLY_x86_64-bin/megahit -t 38 --no-mercy -1 270B_R_1P.fastq,500B_R_1P.fastq,800B_R_1P.fastq,3k_1_R_1P.fastq,5k-1_R_1P.fastq,5k-2_R_1P.fastq,10k_R_1P.fastq -2 270B_R_2P.fastq,500B_R_2P.fastq,800B_R_2P.fastq,3k_1_R_2P.fastq,5k-1_R_2P.fastq,5k-2_R_2P.fastq,10k_R_2P.fastq

/software/SOAPdenovo2-r241/SOAPdenovo-fusion -D -s config -p 40 -K 63 -g k63 -c ../megahit_out/final.contigs.fa
/software/SOAPdenovo2-r241/SOAPdenovo-127mer map -s config -p 40 -g k63
/software/SOAPdenovo2-r241/SOAPdenovo-127mer scaff -p 40 -g k63

/software/megahit_v1.1.1_LINUX_CPUONLY_x86_64-bin/megahit -t 20 --no-mercy -1 500B_R_1P.fastq,800B_R_1P.fastq,3k_1_R_1P.fastq,5k-1_R_1P.fastq,5k-2_R_1P.fastq,10k_R_1P.fastq -2 500B_R_2P.fastq,800B_R_2P.fastq,3k_1_R_2P.fastq,5k-1_R_2P.fastq,5k-2_R_2P.fastq,10k_R_2P.fastq -o megahit_out.no270

/software/SOAPdenovo2-r241/SOAPdenovo-fusion -D -s config -p 40 -K 63 -g k63_1 -c ../megahit_out.no270/final.contigs.fa
/software/SOAPdenovo2-r241/SOAPdenovo-127mer map -s config -p 40 -g k63_1
/software/SOAPdenovo2-r241/SOAPdenovo-127mer scaff -p 40 -g k63_1

#maximal read length
max_rd_len=151
[LIB]
avg_ins=500
reverse_seq=0
asm_flags=2
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=500B_R1.fastq
q2=500B_R2.fastq
[LIB]
#average insert size
avg_ins=800
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=2
#in which order the reads are used while scaffolding
rank=3
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=800B_R1.fastq
q2=800B_R2.fastq
[LIB]
avg_ins=3000
reverse_seq=1
asm_flags=2
rank=3
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=4
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=3k_1_R1.fastq
q2=3k_1_R2.fastq
[LIB]
avg_ins=5000
reverse_seq=1
asm_flags=2
rank=4
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=5k-1_R1.fastq
q2=5k-1_R2.fastq
[LIB]
avg_ins=5000
reverse_seq=1
asm_flags=2
rank=4
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=5k-2_R1.fastq
q2=5k-2_R2.fastq
[LIB]
avg_ins=10000
reverse_seq=1
asm_flags=2
rank=5
# cutoff of pair number for a reliable connection (at least 5 for large insert size)
pair_num_cutoff=5
#minimum aligned length to contigs for a reliable read location (at least 35 for large insert size)
map_len=35
q1=10k_R1.fastq
q2=10k_R2.fastq

All contigs loaded.
Mapping & Scaffolding module.
[main]Data prepare mode selected .

Version 2.04: released on July 13th, 2012
Compile Mar 19 2017	10:58:55

********************
Map
********************

Parameters: map -s config -p 40 -g k63_1 

Kmer size: 63.
Contig length cutoff: 65.

782765 contig(s), maximum sequence length 61533, minimum sequence length 200, maximum name length 10.
Time spent on parsing contigs file: 1s.
40 thread(s) initialized.
Time spent on hashing contigs: 43s.
546166365 node(s) allocated, 630731530 kmer(s) in contigs, 630731530 kmer(s) processed.
Time spent on graph construction: 44s.

Time spent on aligning long reads: 0s.

In file: config, max seq len 151, max name len 256
40 thread(s) initialized.
1565513 edge(s) in the graph.
Import reads from file:
 500B_R1.fastq
Import reads from file:
 500B_R2.fastq
Current insert size is 500, map_len is 32.
--- 100000000th reads.
Import reads from file:
 800B_R1.fastq
Import reads from file:
 800B_R2.fastq
Current insert size is 800, map_len is 32.
--- 200000000th reads.
Import reads from file:
 3k_1_R1.fastq
Import reads from file:
 3k_1_R2.fastq
Current insert size is 3000, map_len is 35.
--- 300000000th reads.
Import reads from file:
 5k-1_R1.fastq
Import reads from file:
 5k-1_R2.fastq
Current insert size is 5000, map_len is 35.
--- 400000000th reads.
--- 500000000th reads.
Import reads from file:
 5k-2_R1.fastq
Import reads from file:
 5k-2_R2.fastq
Current insert size is 5000, map_len is 35.
--- 600000000th reads.
Import reads from file:
 10k_R1.fastq
Import reads from file:
 10k_R2.fastq
Current insert size is 10000, map_len is 35.
--- 700000000th reads.

Total reads         776836032
Reads in gaps       183984010
Ratio               23.7%
Reads on contigs    420553855
Ratio               54.1%
6 pe insert size, the largest boundary is 776836032.

LIB(s) information:
 [LIB] 0, avg_ins 500, reverse 0.
 [LIB] 1, avg_ins 800, reverse 0.
 [LIB] 2, avg_ins 3000, reverse 1.
 [LIB] 3, avg_ins 5000, reverse 1.
 [LIB] 4, avg_ins 5000, reverse 1.
 [LIB] 5, avg_ins 10000, reverse 1.
Time spent on aligning reads: 6541s.

Overall time spent on alignment: 109m.


Version 2.04: released on July 13th, 2012
Compile Mar 19 2017	10:58:55

********************
Scaff
********************

Parameters: scaff -p 40 -g k63_1 

k63_1.Arc: no such file or empty file!

There are 6 grad(s), 776836032 read(s), max read len 151.
Kmer size: 63
There are 1565513 edge(s) in edge file.
Mask contigs with coverage lower than 0.3 or higher than 6.0, and strict length 0.
Average contig coverage is 3, 0 contig(s) masked.
Mask contigs shorter than 65, 0 contig(s) masked.
0 arc(s) loaded, average weight is 0.
/opt/gridview//pbs/dispatcher/mom_priv/jobs/23301.admin.SC: line 19: 72517 Segmentation fault (core dumped) /home/software/SOAPdenovo2-r241/SOAPdenovo-127mer scaff -p 40 -g k63_1               (core dumped) /home/software/SOAPdenovo2-r241/SOAPdenovo-127mer scaff -p 40 -g k63_1

Version 2.04: released on July 13th, 2012
Compile Jul 12 2016     07:31:42

********************
Pregraph
********************

Parameters: pregraph -s /vol/assembly/config_Lmig_PE90_20K_insert.txt -K 43 -p 16 -R -o PE90_20K_ins

In /vol/assembly/config_Lmig_PE90_20K_insert.txt, 1 lib(s), maximum read length 90, maximum name length 256.

16 thread(s) initialized.
Import reads from file:
 /vol/libs/SRR764591_1.fasta
Import reads from file:
 /vol/libs/SRR764591_2.fasta
--- 100000000th reads.
--- 200000000th reads.
--- 300000000th reads.
--- 400000000th reads.
--- 500000000th reads.
--- 600000000th reads.
--- 700000000th reads.
--- 800000000th reads.
--- 900000000th reads.
--- 1000000000th reads.
--- 1100000000th reads.

--- 612500000000th reads.
--- 612600000000th reads.
--- 612700000000th reads.
--- 612800000000th reads.
--- 612900000000th reads.
--- 613000000000th reads.
--- 613100000000th reads.
--- 613200000000th reads.
--- 613300000000th reads.
--- 613400000000th reads.
--- 613500000000th reads.
--- 613600000000th reads.
--- 613700000000th reads.
--- 613800000000th reads.

make[1]: Entering directory `/share/SOAPdenovo2/sparsePregraph'
pregraph_sparse_63mer.v1.0.3 cleaning done.
build_graph.cpp: In function ‘void SavingSparseKmerGraph2(hashtable2*, char*)’:
build_graph.cpp:642:42: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( o_ht_idx, "%llu\n", ht->ht_sz );
                                          ^
build_graph.cpp:689:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
   fprintf ( o_ht_idx, "%llu\n", list_sz );
                                         ^
build_graph.cpp:694:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
   fprintf ( o_cov, "%d\t%llu\n", i, cov_hist[i] );
                                                 ^
In file included from build_edge.cpp:28:0:
./inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, "%llx %llx ,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1] );
                                                                        ^
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
build_edge.cpp: In function ‘void RemovingWeakNodesAndEdges2(hashtable2*, int, int, int, size_t*, size_t*)’:
build_edge.cpp:233:63: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘int’ [-Wformat=]
  fprintf ( stderr, "%llu nodes removed.\n", Removed_Nodes_cnt );
                                                               ^
build_edge.cpp:234:63: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘int’ [-Wformat=]
  fprintf ( stderr, "%llu edges removed.\n", Removed_Edges_cnt );
                                                               ^
build_edge.cpp: In function ‘void removeMinorTips(hashtable2*, int, int, int&)’:
build_edge.cpp:283:68: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
    fprintf ( stderr, "%llu tips removed in cycle %d.\n\n", flag, j );
                                                                    ^
build_edge.cpp:288:58: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
    fprintf ( stderr, "Total %llu tips removed.\n", total );
                                                          ^
build_edge.cpp: In function ‘void mask1in1out(hashtable2*)’:
build_edge.cpp:338:56: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( stderr, "Total nodes number: %llu\n", total );
                                                        ^
build_edge.cpp:339:58: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( stderr, "Linear nodes number: %llu\n", linear );
                                                          ^
build_edge.cpp: In function ‘void pirntStack(std::list<stacked_node2*>&)’:
build_edge.cpp:1154:69: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
    { fprintf ( stderr, "%llx , %d ,", ptr->edge->edge, ptr->is_left ); }
                                                                     ^
build_edge.cpp: In function ‘void process_1stack(hashtable2*, int, std::list<stacked_node2*>&, FILE*, std::vector<preedge2>&)’:
build_edge.cpp:1190:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘std::list<stacked_node2*>::size_type {aka long unsigned int}’ [-Wformat=]
   fprintf ( stderr, "only %llu nodes in the stack \n", stack.size() );
                                                                     ^
build_edge.cpp: In function ‘void output_1edge(preEDGE2*, int, FILE*)’:
build_edge.cpp:1283:69: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘std::basic_string<char>::size_type {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, ">length %d,", long_edge->full_edge->size() - K_size );
                                                                     ^
build_edge.cpp:1293:47: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, "%llx %llx,", from[0], from[1] );
                                               ^
build_edge.cpp:1293:47: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
build_edge.cpp:1294:43: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, "%llx %llx,", to[0], to[1] );
                                           ^
build_edge.cpp:1294:43: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
multi_threads.cpp: In function ‘void* threadRoutine(void*)’:
multi_threads.cpp:93:14: error: ‘usleep’ was not declared in this scope
   usleep ( 1 );
              ^
multi_threads.cpp: In function ‘void sendWorkSignal(unsigned char, unsigned char*)’:
multi_threads.cpp:115:15: error: ‘usleep’ was not declared in this scope
   usleep ( 10 );
               ^
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc multi_threads.cpp
In file included from build_preArc.cpp:46:0:
./inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, "%llx %llx ,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1] );
                                                                        ^
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
build_preArc.cpp: In function ‘void build_vertexes(vertex_hash2*, int, char*)’:
build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 4 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
             & ( from_kmer.kmer ) [0], & ( from_kmer.kmer ) [1], & ( to_kmer.kmer ) [0], & ( to_kmer.kmer ) [1], str, &cvg, &bal_ed ); // from_kmer to_kmer is of no use here
                                                                                                                                    ^
build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 5 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 6 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 7 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
build_preArc.cpp:127:132: warning: format ‘%d’ expects argument of type ‘int*’, but argument 10 has type ‘bool*’ [-Wformat=]
build_preArc.cpp: In function ‘void output_preArcs(preArc_array*, char*)’:
build_preArc.cpp:637:26: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
    fprintf ( fp, "%u", i );
                          ^
build_preArc.cpp:649:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
      fprintf ( fp, "%u", i );
                            ^
build_preArc.cpp: In function ‘void process_1read_preArc(preArc_array*, pthread_spinlock_t*, int, vertex_hash2*, int, int, const char*)’:
build_preArc.cpp:785:93: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
        fprintf ( stderr, "ERROR: left edge id found already !new found id %llu \n", left_id );
                                                                                             ^
build_preArc.cpp:860:96: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
        fprintf ( stderr, "ERROR: right edge id found already, new found id %llu !\n", right_id );
                                                                                                ^
build_preArc.cpp: In function ‘void build_preArc_threaded(preArc_array*, vertex_hash2*, int, int, std::vector<std::basic_string<char> >*, int)’:
build_preArc.cpp:1071:39: error: ‘usleep’ was not declared in this scope
   while ( io_ready == 0 ) {usleep ( 1 );}
                                       ^
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc build_preArc.cpp
pregraph_sparse.cpp: In function ‘int call_pregraph_sparse(int, char**)’:
pregraph_sparse.cpp:171:42: error: ‘usleep’ was not declared in this scope
      while ( io_ready == 0 ) {usleep ( 1 );}
                                          ^
pregraph_sparse.cpp:216:79: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
               difftime ( read_time, beg_time ), processed_reads, bucket_count );
                                                                               ^
pregraph_sparse.cpp:216:79: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
pregraph_sparse.cpp:284:42: error: ‘usleep’ was not declared in this scope
      while ( io_ready == 0 ) {usleep ( 1 );}
                                          ^
pregraph_sparse.cpp:317:143: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
     fprintf ( stderr, "Time spent on building graph round 2: %.fs, %llu reads processed\n", difftime ( read_time, beg_time ), processed_reads );
                                                                                                                                               ^
pregraph_sparse.cpp:318:100: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
     fprintf ( stderr, "%llu nodes allocated, %llu kmer-edges allocated.\n", bucket_count, edge_cnt );
                                                                                                    ^
pregraph_sparse.cpp:318:100: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
pregraph_sparse.cpp:342:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘time_t {aka long int}’ [-Wformat=]
   fprintf ( stderr, "Time spent on removing tips: %llus.\n\n", interval );
                                                                         ^
pregraph_sparse.cpp:355:78: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘time_t {aka long int}’ [-Wformat=]
   fprintf ( stderr, "Time spent on constructing edges: %llus.\n\n", interval );
                                                                              ^
pregraph_sparse.cpp:413:83: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘time_t {aka long int}’ [-Wformat=]
   fprintf ( stderr, "Time spent on building vertex indexes: %llus.\n\n", interval );
                                                                                   ^
pregraph_sparse.cpp:487:76: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘time_t {aka long int}’ [-Wformat=]
   fprintf ( stderr, "Time spent on building preArcs: %llus.\n\n", interval );
                                                                            ^
pregraph_sparse.cpp: In function ‘void initenv(int, char**)’:
pregraph_sparse.cpp:504:2: error: ‘optind’ was not declared in this scope
  optind = 1;
  ^
pregraph_sparse.cpp:507:64: error: ‘getopt’ was not declared in this scope
  while ( ( copt = getopt ( argc, argv, "s:o:K:g:z:d:e:p:m:r:R" ) ) != EOF )
                                                                ^
pregraph_sparse.cpp:529:41: warning: format ‘%Lu’ expects argument of type ‘long long unsigned int*’, but argument 3 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
     sscanf ( optarg, "%Lu", &GenomeSize );
                                         ^
Error in command: g++  -c -O4 -fomit-frame-pointer  -D_63MER_ -m64  -I./inc pregraph_sparse.cpp
In file included from convert_soapdenovo.cpp:28:0:
./inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( fp, "%llx %llx ,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1] );
                                                                        ^
./inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
convert_soapdenovo.cpp: In function ‘void convert(char*, int, char*)’:
convert_soapdenovo.cpp:304:127: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 4 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
             & ( from_kmer.kmer ) [0], & ( from_kmer.kmer ) [1], & ( to_kmer.kmer ) [0], & ( to_kmer.kmer ) [1], &cvg, &bal_ed ); // from_kmer to_kmer is of no use here
                                                                                                                               ^
convert_soapdenovo.cpp:304:127: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 5 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
convert_soapdenovo.cpp:304:127: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 6 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
convert_soapdenovo.cpp:304:127: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 7 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]
convert_soapdenovo.cpp:430:89: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
   fprintf ( fout2, "%llx %llx ", ( ( *it ).first.kmer ) [0], ( ( *it ).first.kmer ) [1] );
                                                                                         ^
convert_soapdenovo.cpp:430:89: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]
convert_soapdenovo.cpp:442:96: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
  fprintf ( stderr, "%llu edges and %llu vertexes constructed.\n", edge_counter, vertex_counter );
                                                                                                ^
convert_soapdenovo.cpp:442:96: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘size_t {aka long unsigned int}’ [-Wformat=]
convert_soapdenovo.cpp:253:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets ( line, 1024, fp );
                           ^
convert_soapdenovo.cpp:254:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets ( line, 1024, fp );
                           ^
convert_soapdenovo.cpp:255:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
   fgets ( line, 1024, fp );
                           ^
make[1]: Leaving directory `/share/SOAPdenovo2/sparsePregraph'
make[1]: Entering directory `/share/SOAPdenovo2/standardPregraph'
SOAPdenovo-63mer cleaning done.
attachPEinfo.c: In function ‘connectByPE_grad’:
attachPEinfo.c:472:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
  fprintf ( stderr, " Accumulated connections             %d\n", newCntCounter );
  ^
attachPEinfo.c: In function ‘connectByPE_grad_gz’:
attachPEinfo.c:583:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
  fprintf ( stderr, " Accumulated connections             %d\n", newCntCounter );
  ^
attachPEinfo.c: In function ‘loadPEgrads’:
attachPEinfo.c:105:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets ( line, sizeof ( line ), fp );
         ^
loadPath.c: In function ‘loadPath’:
loadPath.c:91:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf ( fp, "%d", &num1 );
          ^
loadPath.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf ( fp, "%d", &num2 );
           ^
loadPath.c: In function ‘loadPathBin’:
loadPath.c:236:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf ( fp, "%d", &num1 );
          ^
loadPath.c:240:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
    fscanf ( fp, "%d", &num2 );
           ^
loadPreGraph.c: In function ‘loadVertex’:
loadPreGraph.c:121:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   fscanf ( fp, "%llx %llx", & ( word.high ), & ( word.low ) );
          ^
orderContig.c: In function ‘ScafStat’:
orderContig.c:3329:3: warning: unknown conversion type character 0xa in format [-Wformat=]
   fprintf ( fo, "Total_scaffold_length_as_percentage_of_known_genome_size\t%.2f%\n", 100 * ( 1.0 * Size_includeN / known_genome_size ) );
   ^
orderContig.c:3372:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>100 \t%ld\t%.2f%\n", n100 , 100 * ( 1.0 * n100 / Scaffold_Number ) );
  ^
orderContig.c:3373:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>500 \t%ld\t%.2f%\n", n500 , 100 * ( 1.0 * n500 / Scaffold_Number ) );
  ^
orderContig.c:3374:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>1K  \t%ld\t%.2f%\n", n1k   , 100 * ( 1.0 * n1k / Scaffold_Number ) );
  ^
orderContig.c:3375:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>10K \t%ld\t%.2f%\n", n10k , 100 * ( 1.0 * n10k / Scaffold_Number ) );
  ^
orderContig.c:3376:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>100K\t%ld\t%.2f%\n", n100k, 100 * ( 1.0 * n100k / Scaffold_Number ) );
  ^
orderContig.c:3377:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "scaffolds>1M  \t%ld\t%.2f%\n", n1m   , 100 * ( 1.0 * n1m / Scaffold_Number ) );
  ^
orderContig.c:3379:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_A\t%lld\t%.2f%\n", A_num_all, 100 * ( 1.0 * A_num_all / Size_includeN ) );
  ^
orderContig.c:3380:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_C\t%lld\t%.2f%\n", C_num_all, 100 * ( 1.0 * C_num_all / Size_includeN ) );
  ^
orderContig.c:3381:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_G\t%lld\t%.2f%\n", G_num_all, 100 * ( 1.0 * G_num_all / Size_includeN ) );
  ^
orderContig.c:3382:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_T\t%lld\t%.2f%\n", T_num_all, 100 * ( 1.0 * T_num_all / Size_includeN ) );
  ^
orderContig.c:3383:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "GapContent_N\t%lld\t%.2f%\n", N_num_all, 100 * ( 1.0 * N_num_all / Size_includeN ) );
  ^
orderContig.c:3384:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Non_ACGTN\t%lld\t%.2f%\n", Non_ACGTN_all, 100 * ( 1.0 * Non_ACGTN_all / Size_includeN ) );
  ^
orderContig.c:3385:2: warning: unknown conversion type character 0x9 in format [-Wformat=]
  fprintf ( fo, "GC_Content\t%.2f%\t\t(G+C)/(A+C+G+T)\n", 100 * ( 1.0 * ( G_num_all + C_num_all ) / ( A_num_all + C_num_all + G_num_all + T_num_all ) ) );
  ^
orderContig.c:3471:3: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
   fprintf ( fo, "N50_scaffold-NG50_scaffold_length_difference\t%ld\n", abs ( N50 - N50_known ) );
   ^
orderContig.c:3684:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>100 \t%ld\t%.2f%\n", n100 , 100 * ( 1.0 * n100 / Scaffold_Number ) );
  ^
orderContig.c:3685:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>500 \t%ld\t%.2f%\n", n500 , 100 * ( 1.0 * n500 / Scaffold_Number ) );
  ^
orderContig.c:3686:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>1K  \t%ld\t%.2f%\n", n1k      , 100 * ( 1.0 * n1k / Scaffold_Number ) );
  ^
orderContig.c:3687:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>10K \t%ld\t%.2f%\n", n10k , 100 * ( 1.0 * n10k / Scaffold_Number ) );
  ^
orderContig.c:3688:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>100K\t%ld\t%.2f%\n", n100k, 100 * ( 1.0 * n100k / Scaffold_Number ) );
  ^
orderContig.c:3689:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Contig>1M  \t%ld\t%.2f%\n", n1m      , 100 * ( 1.0 * n1m / Scaffold_Number ) );
  ^
orderContig.c:3691:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_A\t%lld\t%.2f%\n", A_num_all, 100 * ( 1.0 * A_num_all / Size_includeN ) );
  ^
orderContig.c:3692:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_C\t%lld\t%.2f%\n", C_num_all, 100 * ( 1.0 * C_num_all / Size_includeN ) );
  ^
orderContig.c:3693:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_G\t%lld\t%.2f%\n", G_num_all, 100 * ( 1.0 * G_num_all / Size_includeN ) );
  ^
orderContig.c:3694:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Nucleotide_T\t%lld\t%.2f%\n", T_num_all, 100 * ( 1.0 * T_num_all / Size_includeN ) );
  ^
orderContig.c:3695:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "GapContent_N\t%lld\t%.2f%\n", N_num_all, 100 * ( 1.0 * N_num_all / Size_includeN ) );
  ^
orderContig.c:3696:2: warning: unknown conversion type character 0xa in format [-Wformat=]
  fprintf ( fo, "Non_ACGTN\t%lld\t%.2f%\n", Non_ACGTN_all, 100 * ( 1.0 * Non_ACGTN_all / Size_includeN ) );
  ^
orderContig.c:3697:2: warning: unknown conversion type character 0x9 in format [-Wformat=]
  fprintf ( fo, "GC_Content\t%.2f%\t\t(G+C)/(A+C+G+T)\n", 100 * ( 1.0 * ( G_num_all + C_num_all ) / ( A_num_all + C_num_all + G_num_all + T_num_all ) ) );
  ^
orderContig.c:3783:3: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘int’ [-Wformat=]
   fprintf ( fo, "N50_contig-NG50_contig_length_difference\t%ld\n", abs ( N50 - N50_known ) );
   ^
orderContig.c: In function ‘scaffolding’:
orderContig.c:4467:3: warning: too many arguments for format [-Wformat-extra-args]
   fprintf ( fp, ">scaffold%d %d %d %d\n", count, score_count, len, num3 + num5, mask_num );
   ^
orderContig.c:4468:3: warning: too many arguments for format [-Wformat-extra-args]
   fprintf ( fo, ">scaffold%d %d %d %d\n", count, score_count, len, num3 + num5, mask_num );
   ^
orderContig.c:4732:2: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘unsigned int’ [-Wformat=]
  fprintf ( stderr, " Longest scaffold                 %lld\n", length_array[count - 1] );
  ^
orderContig.c:4735:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
  fprintf ( stderr, " Average length                   %d\n", total_len / count );
  ^
orderContig.c: In function ‘scaffold_count’:
orderContig.c:4996:2: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘unsigned int’ [-Wformat=]
  fprintf ( stderr, " Longest scaffold                 %lld\n", length_array[count - 1] );
  ^
orderContig.c:4998:2: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘long int’ [-Wformat=]
  fprintf ( stderr, " Scaffold and singleton length    %lld\n", total_len );
  ^
orderContig.c:4999:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
  fprintf ( stderr, " Average length                   %d\n", total_len / count );
  ^
orderContig.c: In function ‘ScafStat’:
orderContig.c:3250:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets ( buf, 4000, fp );
          ^
orderContig.c:3577:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets ( buf, 4000, fp2 );
          ^
orderContig.c: In function ‘PE2Links’:
orderContig.c:5111:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets ( line, lineLen, fp1 );
         ^
orderContig.c: In function ‘Links2Scaf’:
orderContig.c:5304:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  fgets ( line, lineLen, fp );
        ^
prlHashReads.c: In function ‘AIORead’:
prlHashReads.c:745:6: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat=]
      fprintf ( stderr, "Error:%s.\n", errno );
      ^
prlRead2Ctg.c: In function ‘basicContigInfo’:
prlRead2Ctg.c:726:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  fgets ( lldne, sizeof ( lldne ), fp );
        ^
prlRead2Ctg.c:731:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  fgets ( lldne, sizeof ( lldne ), fp );
        ^
read2scaf.c: In function ‘locateReadOnScaf’:
read2scaf.c:305:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  fgets ( line, 1024, fp );
        ^
readseq1by1.c: In function ‘read1seqfq’:
readseq1by1.c:401:10: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets ( str, lineLen, fp ); // pass quality value line
          ^
iterate.c: In function ‘getNewHash’:
iterate.c:604:2: warning: format ‘%lld’ expects argument of type ‘long long int’, but argument 3 has type ‘unsigned int’ [-Wformat=]
  fprintf ( stderr, "%lld edge(s) deleted in length of 0.\n", deletecount );
  ^
iterate.c: In function ‘fresh’:
iterate.c:2156:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
   fprintf ( stderr, "Refresh edge: %d kmer(s) found.\n", newfoundcount );
   ^
iterate.c:2157:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=]
   fprintf ( stderr, "Refresh edge: %d kmer(s) not found.\n", newnotfoundcount );
   ^
make[1]: Leaving directory `/share/SOAPdenovo2/standardPregraph'
standardPregraph/main.o: In function `main':
main.c:(.text.startup+0xff): undefined reference to `call_pregraph_sparse'
collect2: error: ld returned 1 exit status
make: *** [SOAPdenovo-63mer] Error 1

/home/user/bin/SOAPdenovo-63mer: /usr/local/gcc-4.8.1/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /home/user/bin/SOAPdenovo-63mer)
/home/user/bin/SOAPdenovo-63mer: /usr/local/gcc-4.8.1/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/user/bin/SOAPdenovo-63mer)
/home/user/bin/SOAPdenovo-63mer: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /home/user/bin/SOAPdenovo-63mer)