ERROR: the value provided without a flag/option

[chaoyanggu]

Hi, when I used the sortmerna, version 4.3.6, Build Date: Aug 16 2022, I got the following errors:
[process:1434] ERROR: the value provided without a flag/option. Note that e.g. '-ref' or '-reads' have to be used with Each file. See 'sortmerna -h'

I do not know why, and my codes as follows.

./sortmerna --index 0 --threads 20 --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./sortmerna_index/idx/silva-bac-16s-id90-db:./rRNA_databases/silva-bac-23s-id98.fasta,./sortmerna_index/idx/silva-bac-23s-id98-db:./rRNA_databases/silva-arc-16s-id95.fasta,./sortmerna_index/idx/silva-arc-16s-id95-db:./rRNA_databases/silva-arc-23s-id98.fasta,./sortmerna_index/idx/silva-arc-23s-id98-db:./rRNA_databases/silva-euk-18s-id95.fasta,./sortmerna_index/idx/silva-euk-18s-id95-db:./rRNA_databases/silva-euk-28s-id98.fasta,./sortmerna_index/idx/silva-euk-28s-id98-db:./rRNA_databases/rfam-5s-database-id98.fasta,./sortmerna_index/idx/rfam-5s-database-id98-db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./sortmerna_index/idx/rfam-5.8s-database-id98-db --paired_in --reads RNA-10-2.clean.1.fq.paired.fq --reads RNA-10-2.clean.2.fq.paired.fq --aligned RNA-10-2 --sam --fastx --other RNA-10-2.non --log -v -m 61440 --num_alignments 1 --out2

[chaoyanggu]

By the way, I installed the sortmerna by conda, and I can not find the indexdb_rna in my conda environment, can you tell me where can I get it, thank you.

[biocodz]

4.x vs 2.x is quite a bit different. There is no more indexdb_rna. A single binary is used, and the indexing is done automatically (normally), or can be controlled using -index option e.g. -index 0 means to skip indexing (index is assumed to be ready). Each reference file, and each read file has to use a separate -ref or -read flag i.e. your command is not correctly specified.

sortmerna -h will provide more details.
Also, test.jinja has many use examples.

[chaoyanggu]

Thank you for your reply, I used version v2 before, and the v2 version can specify the location of the database and the name or location of the index, because I don't want to index each sample. But the v4 version is very different, I had changed many times but always got the errors,my changed codes as follows, please tell me is it correct or not, if not, how to modify it ?
[process:1434] ERROR: the value provided without a flag/option. Note that e.g. '-ref' or '-reads' have to be used with Each file. See 'sortmerna -h'
sortmerna --threads 20 -ref ./database/silva-bac-16s-id90-db.fasta -reads RNA-10-2.clean.1.fq.paired.fq -reads RNA-10-2.clean.2.fq.paired.fq --aligned RNA-10-2 --sam --fastx --other RNA-10-2.non --log -v -m 61440 --num_alignments 1

[biocodz]

The command looks ok.
Could you please provide the execution trace?

[chaoyanggu]

my execution trace as follows:

[process:1393] === Options processing starts ... ===
Found value:/RNAseq/bin/sortmerna
Found flag: --index
Found value: 0 of previous flag: --index
Found flag: --threads
Found value: 20 of previous flag: --threads
Found flag: --ref
Found value: ./idx/rfam-5.8s-database-id98-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/rfam-5s-database-id98-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-arc-16s-id95-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-arc-23s-id98-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-bac-16s-id90-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-bac-23s-id98-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-euk-18s-id95-db.fasta of previous flag: --ref
Found flag: --ref
Found value: ./idx/silva-euk-28s-id98-db.fasta of previous flag: --ref
Found flag: --workdir
Found value: ./ of previous flag: --workdir
Found flag: --paired_in
Previous flag: --paired_in is Boolean. Setting to True
Found flag: --reads
Found value: RNA-10-2.clean.1.fq.paired.fq of previous flag: --reads
Found flag: --reads
Found value: RNA-10-2.clean.2.fq.paired.fq of previous flag: --reads
Found flag: --aligned
Found value: RNA-10-2 of previous flag: --aligned
Found flag: --sam
Previous flag: --sam is Boolean. Setting to True
Found flag: --fastx
Previous flag: --fastx is Boolean. Setting to True
Found flag: --other
Found value: RNA-10-2.non of previous flag: --other
Found value: --log

[process:1434] ESC[0;31mERRORESC[0m: the value provided without a flag/option. Note that e.g. '-ref' or '-reads' have to be used with Each file. See 'sortmerna -h'

and the codes was: 
/RNAseq/bin/sortmerna --index 0  --threads 20  --ref ./idx/rfam-5.8s-database-id98-db.fasta  --ref ./idx/rfam-5s-database-id98-db.fasta  --ref ./idx/silva-arc-16s-id95-db.fasta  --ref ./idx/silva-arc-23s-id98-db.fasta  --ref ./idx/silva-bac-16s-id90-db.fasta  --ref ./idx/silva-bac-23s-id98-db.fasta  --ref ./idx/silva-euk-18s-id95-db.fasta  --ref ./idx/silva-euk-28s-id98-db.fasta  --workdir ./   --paired_in   --reads  RNA-10-2.clean.1.fq.paired.fq   --reads  RNA-10-2.clean.2.fq.paired.fq    --aligned RNA-10-2  --sam  --fastx --other RNA-10-2.non --log  -v  --num_alignments 1  --out2

ls idx
rfam-5.8s-database-id98-db.bursttrie_0.dat  silva-arc-16s-id95-db.stats            silva-bac-23s-id98-db.pos_0.dat
rfam-5.8s-database-id98-db.fasta            silva-arc-23s-id98-db.bursttrie_0.dat  silva-bac-23s-id98-db.stats
rfam-5.8s-database-id98-db.kmer_0.dat       silva-arc-23s-id98-db.fasta            silva-euk-18s-id95-db.bursttrie_0.dat
rfam-5.8s-database-id98-db.pos_0.dat        silva-arc-23s-id98-db.kmer_0.dat       silva-euk-18s-id95-db.fasta
rfam-5.8s-database-id98-db.stats            silva-arc-23s-id98-db.pos_0.dat        silva-euk-18s-id95-db.kmer_0.dat
rfam-5s-database-id98-db.bursttrie_0.dat    silva-arc-23s-id98-db.stats            silva-euk-18s-id95-db.pos_0.dat
rfam-5s-database-id98-db.fasta              silva-bac-16s-id90-db.bursttrie_0.dat  silva-euk-18s-id95-db.stats
rfam-5s-database-id98-db.kmer_0.dat         silva-bac-16s-id90-db.fasta            silva-euk-28s-id98-db.bursttrie_0.dat
rfam-5s-database-id98-db.pos_0.dat          silva-bac-16s-id90-db.kmer_0.dat       silva-euk-28s-id98-db.fasta
rfam-5s-database-id98-db.stats              silva-bac-16s-id90-db.pos_0.dat        silva-euk-28s-id98-db.kmer_0.dat
silva-arc-16s-id95-db.bursttrie_0.dat       silva-bac-16s-id90-db.stats            silva-euk-28s-id98-db.pos_0.dat
silva-arc-16s-id95-db.fasta                 silva-bac-23s-id98-db.bursttrie_0.dat  silva-euk-28s-id98-db.stats
silva-arc-16s-id95-db.kmer_0.dat            silva-bac-23s-id98-db.fasta
silva-arc-16s-id95-db.pos_0.dat             silva-bac-23s-id98-db.kmer_0.dat

[chaoyanggu]

I solved my problem because the option --log belongs to the v2 version, not the v4. Now I can run my codes normally. Thank you very much for your help.

[biocodz]

Good to hear you have solved the problem.

I'll note to provide a better options validation, and a more informative error message in the next version