User: Rayan Chikhi
Rayan Chikhi • 1.4k
- Reputation:
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- France, Lille, CNRS
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- 3 weeks, 2 days ago
- Joined:
- 6 years, 5 months ago
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Posts by Rayan Chikhi
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... Hi,
Segfault is unlikely a memory error but rather a bug in the program or something else. Do you have enough disk space? Would it be possible to share the input data?
Best,
Rayan ...
written 6 months ago by
Rayan Chikhi • 1.4k
1
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Comment:
C: GATB buildNode giving errors
... Hi, sorry I didn't get notified by the responses in this thread. In the future, please reach me at rayan.chikhi@univ-lille.fr if this happens!
1) Are you using the Graph or GraphUnitigs class? (seems that it is GraphUnitigs)
2) If you're using GraphUnitigs, the function you're looking for is debug ...
written 6 months ago by
Rayan Chikhi • 1.4k
2
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256
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Answer:
A: GATB buildNode giving errors
... Hi, could you try changing "Node left" to "auto left" to see if it gets rid of the error?
Best,
Rayan ...
written 7 months ago by
Rayan Chikhi • 1.4k
1
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... I think Bastien wants to know why we think the output of fastq-dump is "wrong". I recall it has to do with how the raw .bax.h5 PacBio files get converted to FASTQ. There seems to be additional step(s) needed in order to split raw reads and avoid chimeric reads. `dextractor` does them, but `fastq-dum ...
written 8 months ago by
Rayan Chikhi • 1.4k
0
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776
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... Have a look at https://github.com/rrwick/Unicycler ...
written 9 months ago by
Rayan Chikhi • 1.4k
5
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1
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1.2k
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... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 10 months ago by
Rayan Chikhi • 1.4k
0
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1
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423
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... Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds? ...
written 11 months ago by
Rayan Chikhi • 1.4k
0
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1
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423
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1
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... Are you running it on a network drive? also, how many threads and free disk space? ...
written 11 months ago by
Rayan Chikhi • 1.4k
3
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1
answer
423
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1
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... Hi, due to the use of HDF5, the intermediate files do not get properly saved during a run, hence it's generally not possible to restart a minia run. What sort of organism took 72+ hours to assemble? This might be a good occasion to use the latest version of minia (https://github.com/GATB/minia, comp ...
written 12 months ago by
Rayan Chikhi • 1.4k
0
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593
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... I'll mention this one, that is a fork of Discovar that was used to assemble a wheat: https://github.com/bioinfologics/w2rap-contigger ...
written 14 months ago by
Rayan Chikhi • 1.4k
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For A: How to determine appropriate value for abundance parameter?
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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For Fast kmer reverse complement code using bit tricks
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For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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