BLAST Database error: No alias or index file found for nucleotide database

[fahadkhokhar]

Hello,

I have followed the instructions to download the required databases, but this problems still persists:

Command executed:

export BLASTDB= export BLASTDB=$BLASTDB:/home/ubuntu/bin/NanoCLUST/db/taxdb blastn -query consensus.fasta -db /home/ubuntu/bin/NanoCLUST/db/16S_ribosomal_RNA -task blastn -dust no -outfmt "10 sscinames staxids evalue length pident" -evalue 11 -max_hsps 50 -max_target_seqs 5 | sed 's/,/;/g' > consensus_classification.csv

DECIDE FINAL CLASSIFFICATION

cat 11_draft.log > 11_blast.log echo -n ";" >> 11_blast.log BLAST_OUT=$(cut -d";" -f1,2,4,5 consensus_classification.csv | head -n1) echo $BLAST_OUT >> 11_blast.log

Command exit status: 2

Command output: (empty)

Command error: BLAST Database error: No alias or index file found for nucleotide database [/home/ubuntu/bin/NanoCLUST/db/16S_ribosomal_RNA] in search path [/media/kraken/NanoCLUST/work/ff/483a7d41cb9ec59d392dda702d6293::/home/ubuntu/bin/NanoCLUST/db/taxdb:]

Work dir: /media/kraken/NanoCLUST/work/ff/483a7d41cb9ec59d392dda702d6293

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[DavidFY-Hub]

你好，

我已经按照说明下载了所需的数据库，但是此问题仍然存在：

命令执行：

导出BLASTDB = 导出BLASTDB = $ BLASTDB：/ home / ubuntu / bin / NanoCLUST / db / taxdb blastn- 查询共识。fasta-db / home / ubuntu / bin / NanoCLUST / db / 16S_ribosomal_RNA -task blastn -dust no -outfmt“ 10个sscinames staxids evalue长度pident“ -evalue 11 -max_hsps 50 -max_target_seqs 5 | sed's /，/; / g'>共识 _分类.csv #DECIDE最终分类 cat 11_draft.log> 11_blast.log echo -n“;” >> 11_blast.log BLAST_OUT = $（cut -d“;” -f1,2,4,5confidence_classification.csv | head -n1） echo $ BLAST_OUT >> 11_blast.log

命令退出状态： 2

命令输出：（ 空）

命令错误： BLAST数据库错误：在搜索路径[/ media / kraken / NanoCLUST / work / ff / 483a7d41cb9ec59d392dda702d6293 :: / home中，找不到核苷酸数据库[/ home / ubuntu / bin / NanoCLUST / db / 16S_ribosomal_RNA]的别名或索引文件/ ubuntu / bin / NanoCLUST / db / taxdb：]

工作目录： / media / kraken / NanoCLUST / work / ff / 483a7d41cb9ec59d392dda702d6293

提示：解决问题后，可以继续执行，将选项添加-resume到运行命令行

you can try the ” docter“

[genomicsITER]

Hi. I've updated NanoCLUST. The behaviour of --db and --taxdb parameter has changed.

Now it is assumed that databases are downloaded inside the NanoCLUST dir and they MUST be specified as a relative path (--db "db/16S_ribosomal_RNA" --db "db/taxdb") in the 'nextflow run' command.

fahadkhokhar, This time I'm using the prefix $baseDir in the code instead of giving the full path. I hope this time the db can be found inside the container.

[fahadkhokhar]

Hello, unfortunately still not working. I have tried various options for the --db and --tax entries.

My previous post of the error had an empty path as part of the command executed:

export BLASTDB= export BLASTDB=$BLASTDB:/home/ubuntu/bin/NanoCLUST/db/taxdb

[genomicsITER]

I'm checking if there is a problem with the docker container.

Also, does the db directory contains the following structure? ls db/ 16S_ribosomal_RNA.ndb, 16S_ribosomal_RNA.nnd 16S_ribosomal_RNA.nos 16S_ribosomal_RNA.ntf taxdb.btd 16S_ribosomal_RNA.nhr 16S_ribosomal_RNA.nni 16S_ribosomal_RNA.not 16S_ribosomal_RNA.nto taxdb.bti 16S_ribosomal_RNA.nin 16S_ribosomal_RNA.nog 16S_ribosomal_RNA.nsq taxdb

ls db/taxdb taxdb.btd taxdb.bti

[fahadkhokhar]

Yes that is the exact structure I have

[DavidFY-Hub]

Yes that is the exact structure I have

hi，my db is in NanoCLUST,so

nextflow run NanoCLUST/main.nf \ --reads 'no/*.fastq' -profile docker \ --db db/16S_ribosomal_RNA
--tax db/taxdb/
......

like this is ok

[genomicsITER]

I made it to replicate an error like yours. I solved it mounting the database separatedly in the consensus_classification process. These changes are included in the last commit.

The pipeline should be run the same way (--db "db/16S_ribosomal_RNA" --tax "db/taxdb/")

[fahadkhokhar]

Success! Ran to completion for a single sample - now to run on all 34 :)

Many thanks for resolving this issue!

[genomicsITER]

Thank you for your time. Glad you finally ran the pipeline at 100%.

Feel free to open a new issue if you find any problem analyzing your data.