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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Missing contigs #45

Closed chrisquince closed 5 years ago

chrisquince commented 5 years ago

Some contigs have appeared to have gone missing. For example:

cd /mnt/gpfs/Hackathon/Select_config_strong45_s10B/CoAssembly77/binning/group1/Bin_ini

$DESMAN/scripts/LengthFilter.py /mnt/gpfs/Hackathon/Select_config_strong45_s10B/CoAssembly77/assembly/spades/group1.fasta | grep ">" | sed 's/>//g' | sort > id1.txt

sed '1d' clustering_gt1000_merged.csv | cut -d"," -f1 | sort > id2.txt

diff id1.txt id2.txt

Sebastien-Raguideau commented 5 years ago

Hi Chris, I investigated that and this is a leftover of an issue we corrected during last month. The issue where any contig with no orf on it would be ignored in the binning step because of an erroneous bed file. So it's solved if we rerun STRONG after regenerating
/mnt/gpfs/Hackathon/Select_config_strong45_s10B/CoAssembly77/annotation/group1/group1_C10K_contig.bed It should relaunch any rule whose input depend on this file.
Currently the correct bed file is in the same folder with the name CORRECT_group1_C10K_contig.bed