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rkajitani / MetaPlatanus

De novo metagenome assembler
GNU General Public License v3.0
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Read file exception!! #10

Closed kangxiongbin closed 2 years ago

kangxiongbin commented 2 years ago

Dear Rkajitani, I'm interested in your MetaPlatanus. Recently I run it and encouter a issue.

Command: metaplatanus -IP1 r1.fq r2.fq -ont long_10x_2.fq > log.txt 2>&1 MetaPlatanus version: 1.3.0 Error(2): Error, Read file exception!! Read file exception!! Read file is not FASTA/FASTQ format. Command exited with non-zero status 2 1.63user 0.43system 0:02.07elapsed 99%CPU (0avgtext+0avgdata 19988maxresident)k 0inputs+927960outputs (0major+28471minor)pagefaults 0swaps

My paired-end reads: r1.fq: image

r2.fq: image

Do you know how to address the problem? Thank you very much!

rkajitani commented 2 years ago

Thank you for reporting! Lower cases such as "g" causes the error. Temporarily, the error can be avoided replacing lower cases with upper cases. An easy way is to use seqkit seq -w0 -u. In addition, I fix the code to ignore lower cases, and you can use updated metaplatanus_core (executable).

git clone https://github.com/rkajitani/MetaPlatanus.git
cd MetaPlatanus/src/metaplatanus_core
make
cp metaplatnaus_core /metaplatanus-installation-path/sub_bin/
kangxiongbin commented 2 years ago

Thank you very much! It works.