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kensung-lab / hypo-assembler

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Unable to output assembly results #14

Open xujialupaoli opened 3 months ago

xujialupaoli commented 3 months ago

Thanks for the clear documentation and awesome tool. I can run your sample data successfully. But when I used my own sequencing data, it ran for two weeks with no results. I think I got stuck at some step. Could you please help me find out why the assembly result cannot be output for so long? The sequencing data I use are NGS data and ONT data, and the running command is ./run_all.sh -1 "tp_R1.fq.gz" -2 "tp_R2.fq.gz" -l "pass.all.fq.gz" -t 48 It has been running continuously for 2 weeks, and the terminal output is as shown below

image

joshua-casey commented 3 months ago

Hi xujialupaoli,

Seems like the assembly is stuck on the initial FlyE assembly step.

You can try running flye independently with your set of long reads and see if it finishes, or run another assembler and use hypo-assembler with -d to bypass the initial assembly stpe.

Sincerely, Joshua Casey Darian