Problem with DiscoSNP KISSREADS module

Question

[dahmani_amel]

Hi,

When executing DiscSNP, i got an exeption at the KISSREADS MODULE phase:

    #############################################################
    #################### KISSREADS MODULE #######################
    #############################################################
/home/amelmek/DiscoSnp/build/bin/kissreads2 -predictions discoRes_k_31_c_auto_D_100_P_1_b_0.fa -reads SRR1576548_1.fastq.gz -co discoRes_k_31_c_auto_D_100_P_1_b_0_coherent -unco discoRes_k_31_c_auto_D_100_P_1_b_0_uncoherent -k 31 -size_seeds 26 -index_stride 6 -hamming 1 -genotype -coverage_file discoRes_k_31_c_auto_cov.h5

EXCEPTION: Unable to open bank './ yuw'

there was a problem with kissreads2

HELP!!!

Thanks

Amel

Answer 1

[pierre.peterlongo]

Hi Amel, hi all,

Following an email discussion we found out that discoSnp was called using the following command:

~/DiscoSnp/run_discoSnp++.sh -r filename1.fastq.gz filename2.fastq.gz -out output_SNP

As expressed in the doc (doc directory) the read set(s) to use should be defined using a file of file descriptor, e.g. ~/DiscoSnp/run_discoSnp++.sh -r fof.txt -out output_SNP

Here is as short copy of the documentation:

• Case1: I've a unique read set composed of a unique read file (reads.fq.gz).

fof.txt :

reads.fq.gz

• Case2: I've a unique read set composed of a couple of read files (reads_R1.fq.gz and reads_R2.fq.gz). This may be the case in case of pair end sequencing. fof.txt :

fof_reads.txt

and fof_reads.txt:

reads_R1.fq.gz

reads_R2.fq.gz

• Case3 : I've two read sets each composed of a unique read file: reads1.fq.gz and reads2.fq.gz:

fof.txt:

reads_R1.fq.gz

reads_R2.fq.gz

• Case4: I've two read sets each composed two read files: reads1_R1.fq.gz and reads1_R2.fq.gz and reads2_R1.fq.gz and reads2_R2.fq.gz:

fof.txt:

fof_reads1.txt

fof_reads2.txt

and fof_reads1.txt:

reads1_R1.fq.gz

reads1_R2.fq.gz

and fof_reads2.txt:

reads2_R1.fq.gz

reads2_R2.fq.gz

• And so on...

[GenoMax]

Are you offering a solution for the original question that was asked? If not how is this post related to the original question.

[pierre.peterlongo]

This is actually a solution. The original call to discoSnp from Amel was not using correctly the argument for including read sets. This is why I developed here the way of using this argument.

[GenoMax]

Kudos for figuring that out since the original post did not include any information about how discoSNP was run. If your solution works OP can confirm and accept.

[dahmani_amel]

Thank you so much Pierre, it works perfectly!! :)