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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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spades nanopore #1048

Closed antoine4ucsd closed 1 year ago

antoine4ucsd commented 1 year ago

Description of bug

Hello I am trying to apply spades on merged fastq obtained from nanopore. I have one merged fastq file per sample. I am probably missing something obvious here . I tried the following

spades.py --nanopore  sample_merged.fastq.gz  --careful  -t 16 -m 48  -o ./spades_out/
spades.py --merged  sample_merged.fastq.gz  --careful  -t 16 -m 48  -o ./spades_out/
spades.py --nanopore  sample_merged.fastq.gz --merged  sample_merged.fastq.gz  --careful  -t 16 -m 48  -o ./spades_out/

thank you!

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.

Operating System

lnux

Python Version

3.11.0

Method of SPAdes installation

binary

No errors reported in spades.log

asl commented 1 year ago

From manual (https://cab.spbu.ru/files/release3.15.5/manual.html#sec3.1):

To run SPAdes 3.15.5 you need at least one library of the following types: