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DerrickWood / kraken2

The second version of the Kraken taxonomic sequence classification system
MIT License
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Unable to find k2mask in path, can't mask low-complexity sequences #865

Open zrf-cp opened 1 month ago

zrf-cp commented 1 month ago

this is the problem： (czh_env) ./scripts/kraken2-build --standard --threads 24 --db $DBNAME Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences Processed 619 projects (1161 sequences, 1.77 Gbp)... done. All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library...which: no k2mask in (/mnt/hdisk/data2/zrf_data/kraken/kraken2-m aster/scripts:/mnt/hdisk/data2/zrf_data/kraken/kraken2-master/scripts:/home/pathology/anaconda3/envs/czh_env/bin:/home /pathology/anaconda3/condabin:/home/pathology/anaconda3/envs/R4.2.2/bin:/home/pathology/bowtie2/bowtie2-2.4.5-linux-x8 6_64:/home/pathology/IGV/IGV_Linux_2.11.4/jdk-11/bin:/home/pathology/anaconda3/pkgs/subread-2.0.1/bin:/home/pathology/ anaconda3/pkgs/star-2.7.9/bin:/home/pathology/anaconda3/pkgs/trimmomatic-0.39-hdfd78af_2/bin:/home/pathology/anaconda3 /pkgs/fastqc-0.11.9-hdfd78af_1/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/patho logy/.local/bin:/home/pathology/bin) Unable to find k2mask in path, can't mask low-complexity sequences

This problem has been bothering me for a long time, I can't sleep for a few days, can someone give me a hint, thank you very much

ChillarAnand commented 1 month ago

How did you install kraken2? @zrf-cp

Try this command and it should print the path

$ which k2mask
/usr/local/bin/k2mask