velvet

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Segmentation Fault (velveth) with Paired End Illumina Data

5

Hello, I submitted velveth.sh on an HPC cluster at my university. I have installed velvet version "velvet-1.2.10". I ran velveth.sh with the following code: `velveth OutputKmer119 119 -shortPaired -fastq -separate...

hollybpalk

velveth results depending on `OMP_NUM_THREADS` and stalling if `OMP_THREAD_LIMIT=1`

3

I'm currently working on the velvet Galaxy wrappers: https://github.com/galaxyproject/tools-iuc/pull/4641 We recently changed our CI to use 2 instead of 1 core. So far we only used `OMP_NUM_THREADS` which produced different...

bernt-matthias

velveth: Word length 33 greater than max allowed value (31).

1

I am trying to run velveth on my paired files but facing the following error: [0.000000] Velvet can't handle k-mers as long as 33! We'll stick to 31 if you...

vasudhajain29

Could you help me ? I'm confused with velvet which need a large physical memory.

3

$ velvetg output -exp_cov auto [0.000001] Reading read set file output/Sequences; [43.817688] 88015946 sequences found [110.015839] Done [218.490050] Reading pre-graph file output/PreGraph [218.490744] Graph has 19624790 nodes and 88015946 sequences...

jzhou65