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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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Stuck in repeat stage for low coverage sample #707

Closed JWDebler closed 3 weeks ago

JWDebler commented 4 weeks ago

Hi,

I have several fungal isolates of the same species at different sequencing depths.

I just noticed that one of them has been stuck at the 'repeat' stage for several hours. I also noticed that this is one of the samples with low coverage at about 24x.

I have started assembly of a different isolate at 100x coverage and it just raced past the repeat stage in a few minutes.

Is this a problem with the low coverage of the particular sample? If so, is there a way around this?

I'm running version 2.9.4

These are the stats for the reads for this sample and the assembly is meant to be 41 mb:

id                  reads          bases           avg_len       N50
duplex .fastq.gz    16,876         59,276,326      3,512.5       4,946
simplex.fastq.gz    212,112        943,499,131     4,448.1       6,320

Cheers, Johannes

JWDebler commented 4 weeks ago

The process eventually finished, but it too several hours for that step alone, while it only takes a minutes for other samples.

DingJingZhi commented 4 weeks ago

[2024-06-04 21:53:18] INFO: Aligning reads to the graph 0% 10% 20% 30% 40% 50% 60% 70% 80% 90%

waiting........

DingJingZhi commented 4 weeks ago

The process eventually finished, but it too several hours for that step alone, while it only takes a minutes for other samples.

the same as you. so I break them, then turn other app

mikolmogorov commented 3 weeks ago

Ok, since the run has finished - I'm assuming this is now resolved. Different stages of assembly may take longer sometimes, depending on the complexity of the sample.