diamond blastx always return error message "Insufficient arguments. Use diamond -h for help"

Question

[rkooliyottil]

Hi, I am trying to use the sequence aligner diamond to identify my differentially expressed genes from an RNAseq data set. I used diamond blastx -p 24 -f tab --seg yes -d nr -q merged.fa -o matches.m8 But always return with an error message. "Insufficient arguments. Use diamond -h for help" Any help is highly appreciated. Rinu

[WouterDeCoster]

And what does diamond -h tell you about the arguments?

[rkooliyottil]

Thanks, This is what I get from diamond -h

Syntax:
  diamond COMMAND [OPTIONS]

Commands:
  makedb        Build diamond database from a FASTA file
  blastp        Align amino acid query sequences against a protein reference database
  blastx        Align DNA query sequences against a protein reference database
  view  View DIAMOND alignment archive (DAA) formatted file

General options:
  -h [ --help ]             produce help message
  -p [ --threads ] arg (=0) number of cpu threads
  -d [ --db ] arg           database file
  -a [ --daa ] arg          DIAMOND alignment archive (DAA) file
  -v [ --verbose ]          enable verbose out
  --version                 display version information
  --log                     enable debug log

Makedb options:
  --in arg                input reference file in FASTA format
  -b [ --block-size ] arg sequence block size in billions of letters 
                          (default=2)

Aligner options:
  -q [ --query ] arg                 input query file
  -k [ --max-target-seqs ] arg (=25) maximum number of target sequences to 
                                     report alignments for
  --top arg (=100)                   report alignments within this percentage 
                                     range of top alignment score (overrides 
                                     --max-target-seqs)
  --compress arg (=0)                compression for output files (0=none, 
                                     1=gzip)
  -e [ --evalue ] arg (=0.001)       maximum e-value to report alignments
  --min-score arg (=0)               minimum bit score to report alignments 
                                     (overrides e-value setting)
  --id arg (=0)                      minimum identity% to report an alignment
  --query-cover arg (=0)             minimum query cover% to report an 
                                     alignment
  --sensitive                        enable sensitive mode (default: fast)
  -c [ --index-chunks ] arg (=4)     number of chunks for index processing
  -t [ --tmpdir ] arg (=/dev/shm)    directory for temporary files
  --gapopen arg (=-1)                gap open penalty, -1=default (11 for 
                                     protein)
  --gapextend arg (=-1)              gap extension penalty, -1=default (1 for 
                                     protein)
  --matrix arg (=blosum62)           score matrix for protein alignment
  --seg arg                          enable SEG masking of queries (yes/no)
  --salltitles                       print full subject titles in output files

Advanced options (0=auto):
  --seed-freq arg (=-15)          maximum seed frequency
  -l [ --run-len ] arg (=0)       mask runs between stop codons shorter than 
                                  this length
  -C [ --max-hits ] arg (=0)      maximum number of hits to consider for one 
                                  seed
  --id2 arg (=0)                  minimum number of identities for stage 1 hit
  -w [ --window ] arg (=0)        window size for local hit search
  --xdrop arg (=20)               xdrop for ungapped alignment
  -X [ --gapped-xdrop ] arg (=20) xdrop for gapped alignment in bits
  --ungapped-score arg (=0)       minimum raw alignment score to continue local
                                  extension
  --hit-band arg (=0)             band for hit verification
  --hit-score arg (=0)            minimum score to keep a tentative alignment
  --band arg (=0)                 band for dynamic programming computation
  -s [ --shapes ] arg (=0)        number of seed shapes (0 = all available)
  --index-mode arg (=0)           index mode (1=4x12, 2=16x9)
  --fetch-size arg (=4096)        trace point fetch size
  --single-domain                 Discard secondary domains within one target 
                                  sequence
  -r [ --no-traceback ]           disable alignment traceback
  --dbsize arg (=0)               effective database size (in letters)

View options:
  -o [ --out ] arg           output file
  -f [ --outfmt ] arg (=tab) output format (tab/sam)
  --forwardonly              only show alignments of forward strand

[WouterDeCoster]

What if you try the example command provided on github,

diamond blastx -d nr -q merged.fa -o matches.m8

[rkooliyottil]

This is what I used the first time, then I added other arguments. But still it is giving the same message. In the mean time, I tried adding another argument -a matches.daa. It seems like working. It produced an output file "matches.daa". Is this my results of Blast? If so, how to read this file?

[GenoMax]

Have you actually created the nr DIAMOND database fromnr.fa file?

[rkooliyottil]

Yes, I did. I am now able to do this. Thank you so much for your help.

[g.feng]

Hi, I am having this problem as well. Could you be able to tell me how did you solve the problem? Thanks.

[GenoMax]

I assume the poster above created nr DIAMOND database, which fixed the problem. Have you done that?

[g.feng]

Yes, I did it. The nr.dmnd is created from nr.faa. Thanks.

[GenoMax]

If the index file is not in your $PATH then make sure you provide the full file path in the command.

diamond blastx -d /full_path_to/nr -q merged.fa -o matches.m8

[g.feng]

Hi, I believe I am working in the file directory. Even I added the full path, it still did not work. May I ask is there a specific format of the DNA sequence file? The manual says "translated DNA". Therefore I used the .fna output file from prokka. I am sorry if I ask silly questions, I am new in bioinformatics. Thanks.

[buchfink]

Please show us your command line and the full console output of Diamond. Also please run this and show us the output: diamond --version

[g.feng]

hi, below are the command lines and the console output. Thanks.

uqgfeng@aw016 ~
$ diamond --version
diamond version 0.7.12

uqgfeng@aw016 ~
$ cd /30days/uqgfeng/diamond/

uqgfeng@aw016 /30days/uqgfeng/diamond
$ diamond makedb --in nr.faa -d nr

uqgfeng@aw016 /30days/uqgfeng/diamond
$ diamond blastx -d nr -q test.fna -o matches.m8
Insufficient arguments. Use diamond -h for help.

uqgfeng@aw016 /30days/uqgfeng/diamond

[buchfink]

Try -a matches.m8. The version you are using is very old though, I recommend upgrading to the latest version.

[g.feng]

Thanks for your suggestion. I am using a server based diamond. I have requested the updation, however, it takes very long time. In the meantime, I did -a matches.m8 which created matches.m8.daa. However, I couldn't open it on my server. Do you have any suggestions to help me open it? Thanks very much for your help.

Answer 1

[buchfink]

Hi, the problem is that you're using a very old version of diamond which had a different syntax, and could only generate DAA files. I recommend upgrading to the latest version.

[rkooliyottil]

Thanks, I am now able to do the process.