Forum:discosnp output on OSX 10.10.1

Question

[rob.lanfear]

Hi,

I downloaded and compiled discoSnp++, and ran the test files no problem. The only (very minor) issue I want to report is that the logging to the screen does not seem to operate quite as intended on my machine (MAC OSX 10.10.1, 1.7GHz Intel Core i7).

It looks like a very minor issue with line breaks (I can see the '/n' in the text output to the stdout during the graph creation). The tabular output for graph creation and other modules is all fine. I've pasted an example of the output below, from the test dataset.

Thanks for making a great tool!

Rob

Mellisuga:DiscoSNP++-2.0.0-Source robertlanfear$ ./run_discoSnp++.sh -r "data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz"

use read set: data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz

Binaries in /Applications/Biocomputing/DiscoSNP++-2.0.0-Source/build/

    Running discoSnp++ 1.0.0, in directory /Applications/Biocomputing/DiscoSNP++-2.0.0-Source with following parameters:
         read_sets=data_sample/reads_sequence1.fasta.gz data_sample/reads_sequence2.fasta.gz
         prefix=discoRes_k_31_c_4
         c=4
         C=2147483647
         k=31
         b=0
         d=1
         D=0
     starting date=Thu 22 Jan 2015 10:29:47 AEDT

    ############################################################
    #################### GRAPH CREATION  #######################
    ############################################################
/Applications/Biocomputing/DiscoSNP++-2.0.0-Source/build//ext/gatb-core/bin/dbgh5 -in data_sample/reads_sequence1.fasta.gz,data_sample/reads_sequence2.fasta.gz -out discoRes_k_31_c_4 -kmer-size 31 -abundance-min 4 -abundance-max 2147483647 -solidity-kind max
[DSK: Collecting stats on read sample   ]  100    %     elapsed:      0 min 0     sec    estimated remaining:      0 min 0     sec  cpu:  133.3 %   mem: [   11,   11,    0] MB 
,e,[ d DS:SSt tKe e:p p    P2 2a: :s 0 sc c omo1uiu/nnn1t t,i0i n nSg gt   ek kpm m ese2rer:scs    c   o] ]u   n e t9s9i.t.n4i4g m   a k t m e e%d%r   s r   e   m ] a  eie lnl9aia.pnp4sgs e:e d d : :    %             0      0m0e I lmnmai ipn0ns   ,,e[  dDSS:Stt Kee :pp     P22 a:: s  0scc  oom1uui/nnn1tt ,ii0 nn Sgg t   ekk pmm  ees2rre:ssc    c   o]] u   n  et99si..tn44ig  m   ak  tm  ee%%dr   s  r   e   m]  a eei lln9aai.ppn4ssge e:d d : :      %              0 0    0emm liimannip  ns00 ,,e[  dDSS:Stt Kee :pp     P22 a:: s  0scc  oom1uui/nnn1tt ,ii0 nn Sgg t   ekk pmm  ees2rre:ssc    c   o]] u   n  et99si..tn44ig  m   ak  tm  ee%%dr   s  r   e   m]  a eei lln9aai.ppn4ssg ee: dd  ::     %               0    00em  limmaniip nns1  e 00d   :            s   ess cee  cc0    c  mp  iu  n:ee  ss0 tt 1ii 4mm 0aa .tt 0ees dde%  c rr  ee  mm maa eiiemnns:iit nni[ggm ::a   t   e4  d1   ,  r   e 00m   a4mmi1iin,nni   n 11g   :    0   ]       Mss Bee  cc0     mccippnuu ::1      11 44 01t[/eD1pS, K 2:S: t Pecapos us2n :t1 i/cn1og,u  nkStmtieenrpgs   2k :m] e cr os1u 8n .t]3i  n  g1  8%k. m3 e  r  s   %e  l] a  p  s1 e8ed.l:3a  p  s  e %d  :   0      m ei ln a 0p0 s me id n:    0 s  e  c       0 s  emecis nt  I 0m  ae ts et di  m S[1tD/eS1pK, : 2 S:Pt aecspos u 2n1:t/ i1cn,og u Snkttmeiepnr gs2  :k  m]ce or us1n 8t .i]3n  g   1 k8%m. e3 r  s      %e] l  a  p1 s8 e.ed3l: a  p  s %e  d  :   0     me il na  p00s  em di :n     0s  e  c      0   s meeicsn t  i0 m  a et se td i:0[ ]DP SaMKsB:s   P1a/s1s,  1S/t1e,p  S2t:e pc o2u:n tcionugn tkimnegr sk m e]r s  1 8]. 3  1 8 .%3       %  e l a p seelda:p s e d :    0   m I n0  0m in 0         sseecc        eessttiimmaatteedd  rreemmaaiinniinngg::            00  mmiinn  00 [P[DaDSsSKsK: : 1 P/Pa1as,ss s S 1t1/e/1p1, , 2 S:St tecepop u 2n2:t: I cncogou unkntmtieinrngsg   k km]me er rs2s 7  . ]7]      2 27%7. .7 7         %e% l  a  p  s  e edel:la ap ps se ed d: : 0     m  I  n    000   m mi in n   0s0 e  c          s seeecsc t  I  m  a etesestdti imrmaeatmteaedid n rirenemgma:ai in ni in ng g: : 0     m  I  n    000   m mi in n   0s0 e  c        c spseuec:c      c1cp5pu7u:.: 1    1%15 57 7. .1m1 e %m% :     [ m me em m:3: 5 [,[         334551,,,         44 11aD[sSDsKS :K1 :/P 1aP,sa ssS st1 e/1p1/ ,12 ,:S  tScetopeu pn2 t:2i :nc goc uoknumtneitrnisgn  g k ]mk em re2sr7 s.  7]   ]    2 %72 . 77 .  7    e %l  a% p  s  e  d e: l ea lp as pe sd e:0d  : m  I  n     0 0    0m  I mn I sn0e  c0            se esscte ic m  a  t ee sdet sirtmeiammtaaeitdne idrn egrm:ea mi an ii nn ig n:0g  : m  I  n     0 0    0m  I mn I sn0e  c0       c  p su e:sc e  c 1 c3 p7cu.p:5u  : % 1  3 17 3.m75e. m5%:   % [    m  e mm3e:5m ,:[    [    4 31 5,3, 5  ,      40 1]4,[s[D DS1SK/K:1: , P PaSastsses p 1 1/2/1:1, , c SoStuteneptp I 2n2:g:   ckcomoueunrntsti in ng]g   k km2me7er.rs7s      ] ] %    2 27 7. .7 7 e  l  a %p% s  e  d  :    e el la ap ps se0ed d:m: I  n     0       0 0   m misinen c 0 0          e  s stseiecmc a  t  e  d e esrstetimimamaiatnteiednd g r:re em ma ai in ni in0ng g:m: I  n     0       0 0   m

etc...

Answer 1

[pierre.peterlongo]

Hi Rob,

Thanks for this feedback.

Indeed, there is still a display problem due to parallelization, and specifically on mac OS. We'll fix this as soon as possible.

Pierre

[rob.lanfear]

Just in case it helps, with the latest version (2.0.1) I still see the same odd output with the test dataset. But with my own data (much larger, and just running on a small laptop for now) I see very nicely formatted output with expected times to completion that update (e.g. pasted below).

Cheers,
Rob

Mellisuga:DiscoSNP++-2.0.1-Source robertlanfear$ ./run_discoSnp++.sh -r "data_sample/M1a_index2_CGATGTAT_L003_R1_001.fastq.gz data_sample/M7a_index7_CAGATCAT_L006_R1_001.fastq.gz" -T

use read set: data_sample/M1a_index2_CGATGTAT_L003_R1_001.fastq.gz data_sample/M7a_index7_CAGATCAT_L006_R1_001.fastq.gz

Binaries in /Volumes/Lanfear_data/DiscoSNP++-2.0.1-Source/build/

    Running discoSnp++ 1.0.0, in directory /Volumes/Lanfear_data/DiscoSNP++-2.0.1-Source with following parameters:

         read_sets=data_sample/M1a_index2_CGATGTAT_L003_R1_001.fastq.gz data_sample/M7a_index7_CAGATCAT_L006_R1_001.fastq.gz
         prefix=discoRes_k_31_c_4
         c=4
         C=2147483647
         k=31
         b=0
         d=1
         D=0
     starting date=Fri 23 Jan 2015 14:14:03 AEDT
    ############################################################
    #################### GRAPH CREATION  #######################
    ############################################################

/Volumes/Lanfear_data/DiscoSNP++-2.0.1-Source/build//ext/gatb-core/bin/dbgh5 -in data_sample/M1a_index2_CGATGTAT_L003_R1_001.fastq.gz,data_sample/M7a_index7_CAGATCAT_L006_R1_001.fastq.gz -out discoRes_k_31_c_4 -kmer-size 31 -abundance-min 4 -abundance-max 2147483647 -solidity-kind max
[DSK: Collecting stats on read sample   ]  100    %     elapsed:      0 min 10    sec    estimated remaining:      0 min 0     sec  cpu:  180.1 %   mem: [   18,   18,    0] MB 
[DSK: Pass 1/1, Step 2: counting kmers  ]  100    %     elapsed:     13 min 12    sec    estimated remaining:      0 min 0     sec  cpu:  146.2 %   mem: [   74, 1586,    0] MB 
[Bloom: read solid kmers                ]  100    %     elapsed:      2 min 10    sec    estimated remaining:      0 min 0     sec  cpu:   93.7 %   mem: [  278,  278,    0] MB 
[Debloom: build extension               ]  7.14   %     elapsed:      0 min 28    sec    estimated remaining:      6 min 0     sec  cpu:  143.8 %   mem: [  384,  384,    0] MB

Answer 2

[pierre.peterlongo]

Hi Rob,

The display problem should be fixed now. The last 2.0.2 version corrects this issue. http://http://colibread.inria.fr/files/2013/10/DiscoSNPpp-2.0.2-Source.zip

Thanks again for your feedbacks.

Pierre