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DessimozLab / read2tree

a tool for inferring species tree from sequencing reads
MIT License
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error when map rna-seq to OMA db #31

Closed catslu closed 1 year ago

catslu commented 1 year ago

Dear developers, I had installed r2t by conda, downloaded the markers of Mollusca with 3 species genome via OMA db online. Now I am testing r2t using Mytilus spp. transcriptome data, only one paired , generated by illunima Noveseq 6000 platform with 150bp x2，i running with follow: read2tree --tree --standalone_path ../others_rna/r2t/ --reads SCK-1.trim_1.fq.gz SCK-2.trim_2.fq.gz --threads 40 --output_path ./r2t_test

for warning : 2023-06-19 12:38:35,686 - read2tree.Mapper - INFO - SCK-1: --- Mapping of reads to CRAGI reference species --- /home/gene/liuxl/miniconda3/envs/sc/lib/python3.10/subprocess.py:959: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdout = io.open(c2pread, 'rb', bufsize) /home/gene/liuxl/miniconda3/envs/sc/lib/python3.10/subprocess.py:964: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stderr = io.open(errread, 'rb', bufsize)

warning is ok?

sinamajidian commented 1 year ago

Hi @catslu Thanks for using Reed2Tree. Yes, this warning is fine and you can ignore it.

Best regards, Sina