bcalm
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GATB
compacted de Bruijn graph construction in low memory
Hello, I am running `bcalm` as part of the spacegraph cats pipeline in collaboration with @taylorreiter. The command I am running is: `bcalm -in INFILES -out OUTFILE -kmer-size 31 -abundance-min...
``bcalm -version`` returns an error code 1 to the shell, causing pipelines like **snakemake** to break.
Anton reported that it crashes with: ``` unexpected problem: repart bucket unexpected problem: repart bucket unexpected problem: repart bucket ```` I'll investigate someday.
BCALM doesn't crash nicely when the input is an incorrect fasta file. The current error message is: ``` >cat blin.fa adfad > bcalm -in blin.fa -kmer-size 3 BCALM 2, git...
BCALM2 does not always crash elegantly when the input fasta. For example, ``` >cat blin.fa adfad > bcalm -in blin.fa -kmer-size 3 BCALM 2, git commit e9ba83c setting storage type...
I'm trying to run BCALM on a very large database and I keep getting errors that look like: ``` mem: [ 100, 91622, 92822] MB EXCEPTION: Pool reserve() failed for...
Error: libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
* OS: OS X * Command: `bcalm -in "hg38/hg38.fna" -out "hg38/hg38.bc31.fa" -kmer-size "31" -nb-cores "1" -abundance-min 1` * Dataset: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz ``` BCALM 2, git commit c8ac60252fa0b2abf511f7363cff7c4342dac2ee setting storage type to...
on only one cluster (Paris-Sud), that error occurs right at the beginning of k-mer counting. Then it crashes with `EXCEPTION: Unable to load Repartitor (minimRepart), possibly due to bad format.`...
In the [description](https://github.com/GATB/bcalm/blob/master/bidirected-graphs-in-bcalm2/bidirected-graphs-in-bcalm2.md) of how bi-directed graphs are implemented in bcalm2, it would be nice to add another example to the "Bi-directed de Bruijn graph section." Currently, the example there...