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mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs
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minimap2 and samtools issues in running consensus stage #698

Closed Jerry-is-a-mouse closed 1 month ago

Jerry-is-a-mouse commented 2 months ago

Hi fenderglass, I installed Flye version 2.9.3-b1797 through conda in a independent env, and ran it in command nohup time -v flye --nano-raw /public/share/wrj23/phasing/data/ont/HG002.nanopore.fastq --out-dir /public/share/wrj23/phasing/flye_nanopore/ --no-alt-contigs --threads 128 1> /public/share/wrj23/phasing/flye_nanopore/flye.nanopore.1.log 2> /public/share/wrj23/phasing/flye_nanopore/flye.nanopore.2.log & But it failed again and again, and time comsuming. Here are the flye.log and minimap.stderr. flye.nanopore.2.log minimap.stderr.log I have difficulty in dealing with it.

mikolmogorov commented 1 month ago

Something is wrong with your Flye installation - minimap2 log says that it can't find the executable. I recommend a fresh install in a new bioconda environment. Hope this helps!