DiscoSNP++ 2.2.0 problem

Question

[tkitapci]

Hi,

I can run discoSNP 2.1.7 but I am trying to run discoSNP 2.2.0. The compilation was successful when I run the simple_test.sh I get this: (test files are downloaded successfully and they are in the same directory)

use read set: ./ERR39478.fastq.gz ./SRR387476.fastq.gz
use at most 1 cores
./run_discoSnp++.sh: line 242: ${read_sets}_removemeplease: ambiguous redirect
Binaries in /home/cmb-02/sn1/tkitapci/software/DiscoSNP++-2.2.0-Source/build/
        Running discoSnp++ 2.2.1, in directory /home/cmb-02/sn1/tkitapci/software/DiscoSNP++-2.2.0-Source with following parameters:
                 read_sets=./ERR039477.fastq.gz ./SRR387476.fastq.gz
                 prefix=discoRes_k_31_c_auto
                 c=auto
                 C=2147483647
                 k=31
                 b=0
                 d=1
                 D=100
         starting date=Fri Sep  4 13:56:24 PDT 2015

        ############################################################
        #################### GRAPH CREATION  #######################
        ############################################################
/home/cmb-02/sn1/tkitapci/software/DiscoSNP++-2.2.0-Source/build//ext/gatb-core/bin/dbgh5 -in ./ERR039477.fastq.gz ./SRR387476.fastq.gz_removemeplease -out discoRes_k_31_c_auto -kmer-size 31 -abundance-min auto -abundance-max 2147483647 -solidity-kind one -nb-cores 1
ERROR: Unknown parameter './SRR387476.fastq.gz_removemeplease'

[graph options]

   [kmer count options]
          -in                      (1 arg) :    reads file
          -kmer-size               (1 arg) :    size of a kmer  [default '31']
          -abundance-min           (1 arg) :    min abundance threshold for solid kmers  [default '3']
          -abundance-max           (1 arg) :    max abundance threshold for solid kmers  [default '2147483647']
          -abundance-min-threshold (1 arg) :    min abundance automatic threshold  [default '3']
          -histo-max               (1 arg) :    max number of values in kmers histogram  [default '10000']
          -solidity-kind           (1 arg) :    way to compute solids (sum, min, max, one, all)  [default 'sum']
          -max-memory              (1 arg) :    max memory (in MBytes)  [default '2000']
          -max-disk                (1 arg) :    max disk   (in MBytes)  [default '0']
          -solid-kmers-out         (1 arg) :    output file for solid kmers  [default '']
          -out                     (1 arg) :    output file  [default '']
          -out-dir                 (1 arg) :    output directory  [default '.']
          -minimizer-type          (1 arg) :    minimizer type (0=lexi, 1=freq)  [default '0']
          -minimizer-size          (1 arg) :    size of a minimizer  [default '8']
          -repartition-type        (1 arg) :    minimizer repartition (0=unordered, 1=ordered)  [default '0']

   [bloom options]
          -bloom        (1 arg) :    bloom type ('basic', 'cache', 'neighbor')  [default 'neighbor']
          -debloom      (1 arg) :    debloom type ('none', 'original' or 'cascading')  [default 'cascading']
          -debloom-impl (1 arg) :    debloom impl ('basic', 'minimizer')  [default 'minimizer']

   [branching options]
          -branching-nodes (1 arg) :    branching type ('none' or 'stored')  [default 'stored']
          -topology-stats  (1 arg) :    topological information level (0 for none)  [default '0']

   [emphf options]
          -mphf (1 arg) :    mphf type ('none' or 'emphf')  [default 'none']

   [general options]
          -nb-cores          (1 arg) :    number of cores  [default '0']
          -verbose           (1 arg) :    verbosity level  [default '1']
          -integer-precision (1 arg) :    integers precision (0 for optimized value)  [default '0']

          -email             (1 arg) :    send statistics to the given email address  [default '']
          -email-fmt         (1 arg) :    'raw' or 'xml'  [default 'raw']
          -check             (1 arg) :    check result with previous result  [default '']
          -check-dump        (1 arg) :    dump some properties of the created graph into a file  [default '']
there was a problem with graph construction
md5sum: discoRes_k_31_c_4_D_0_P_1_b_0_withlow_coherent.fa: No such file or directory
md5sum: discoRes_k_31_c_4_D_0_P_1_b_0_withlow_uncoherent.fa: No such file or directory
md5sum: discoRes_k_31_c_4_D_0_P_1_b_0_withlow_coherent.vcf: No such file or directory
1d0
< eb49fdefddd8627eeecc427b9b4ce7c5  discoRes_k_31_c_4_D_0_P_1_b_0_withlow_coherent.fa
TEST 1 KO
1d0
< 3fd37576255360df6206debebb6a3f16  discoRes_k_31_c_4_D_0_P_1_b_0_withlow_uncoherent.fa
TEST 2 KO
1d0
< ead4f4d85b1596648a6e35364de62c69  discoRes_k_31_c_4_D_0_P_1_b_0_withlow_coherent.vcf
TEST 3 KO

Thanks for the help!

Answer 1

[h.mon]

From DiscoSNP++ site:

17/07/2015: Important update - DiscoSNP++-2.2.0

Input read set format has changed. Use now file of files. This provides an easier way of dealing with read sets composed of several read files (pair end or pools). See the documentation in the doc directory

It seems you have to use -r to indicate the "file of files".

[pierre.peterlongo]

That's it, thanks :)