mikolmogorov/Flye

minimap2 and samtools issues in running consensus stage

Jerry-bioinformatics opened this issue · 1 comments

Jerry-bioinformatics commented

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

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!