DBGraph.fasta not generated

[Arkhaan]

Hi, When running brownie with the following command : brownie graphConstruction -k 71 -t 12 -o DBGraph.fasta reads.fastq

The software stops at stage 4 and does not enter stage 5, thus not giving the correct output. Or is it something I missed?

Edit : I found in the code that with the graphConstruction command, the stage 5 is skipped. Is this the intended behavior?

[Arkhaan]

On a related note, removing the graphConstruction command on the line above allows to enter stage 5, however brownie crashes with a Segmentation fault. It happens at this moment : From log Creating graph... done (1min 7s) Graph contains 16416137 nodes and 45580292 arcs Creating kmer lookup table... done (23min 34s) Building suffix array (sparseness factor: 1)... From error bash: line 1: 38740 Segmentation fault (core dumped) brownie -k 31 -t 12 -o DBGraph.fasta files.fastq

[gmiclotte]

Hello,

If you want the DBGraph.fasta file, i.e. the corrected de Bruijn graph in fasta format, then run brownie graphConstruction -k 71 -t 12 reads.fastq The -o option is used to specify the corrected reads output file.

Correcting reads happens in stage 5, if you just want the corrected de Bruijn graph, then you only need stages 1-4.

If brownie crashes while building the suffix array in stage 5, then try running with a higher sparseness factor (specified with option -e or --essa, default is 1, try -e 2 or higher).

Kind regards, Giles

[Arkhaan]

Thank you, it looks like I misinterpreted how to use it! I am running it again, with correct parameters this time.