kuangzhuoran
commented
2 years ago I think I have solved this today. First I download Stardard database on ' https://benlangmead.github.io/aws-indexes/k2 ' and tar -zxvf xxxx Then download 'taxonomy' to the same directory by (kraken2-build --threads 30 --db ./ --download-taxonomy)
It works perfectly~ (kraken2 --db kraken2_DB -t 5 --report ./$i.report -output ./$i.txt ./$i.fasta)
But I have 1 question.
The first is what I should do if I want to use more databases instead of just Standard. cat all the file which have the same name (hash.k2d...) unzipped from different databases?
(PS:when I use "metawrap2 kraken2", It will report an error “KeyERROR : 1418105” (Different samples have different numbers))
Hi ！
I first changed the rsync_from_ncbi.pl script due to the error that many people having on #508
Then I encountered an error in the title，My command is "kraken2-build --standard --threads 6 --db MY_KRAKEN2_DB" So I changed '--threads' (followed the error prompt)，Only the number in the error will change and the rest will be the same：
Masking low-complexity regions of downloaded library... done. build_db: OMP only wants you to use x threads （only x changed） xargs: cat: terminated by signal 13
I had noticed "Error: OMP wants to use only 1 thread #348" Then I added "unset OMP_NUM_THREADS" to my script, so its like 2 lines: unset OMP_NUM_THREADS kraken2-build --standard --threads 6 --db MY_KRAKEN2_DB The error is the same (as above) : build_db: OMP only wants you to use 3 threads
Next I try #139 add this line to the job script “export OMP_NUM_THREADS= 6”；it didnt work，Error reporting was the same, but there would be several lines of "slurm_script: line 9: export: `6': not a valid identifier" and "libgomp: Invalid value for environment variable OMP_NUM_THREADS" .
I found that I can download the database directly through "https://benlangmead.github.io/aws-indexes/k2", So maybe there are other ways to build a kraken2 database?
The following is the log file
Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library... done. Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library... done. Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Masking low-complexity regions of downloaded library... done. Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Step 2/2: Assigning taxonomic IDs to sequences All files processed, cleaning up extra sequence files... done, library complete. Downloading UniVec_Core data from server... done. Adding taxonomy ID of 28384 to all sequences... done. Masking low-complexity regions of downloaded library... done. build_db: OMP only wants you to use 3 threads (1，2，3，4，5，6) xargs: cat: terminated by signal 13