Question: diamond blastx always return error message "Insufficient arguments. Use diamond -h for help"
0
gravatar for rkooliyottil
22 months ago by
rkooliyottil0 wrote:

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

rna-seq • 1.1k views
ADD COMMENTlink modified 22 months ago by buchfink100 • written 22 months ago by rkooliyottil0

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

ADD REPLYlink written 22 months ago by WouterDeCoster35k

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
ADD REPLYlink modified 22 months ago by WouterDeCoster35k • written 22 months ago by rkooliyottil0

What if you try the example command provided on github,

diamond blastx -d nr -q merged.fa -o matches.m8
ADD REPLYlink written 22 months ago by WouterDeCoster35k

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?

ADD REPLYlink written 22 months ago by rkooliyottil0

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

ADD REPLYlink written 22 months ago by genomax59k

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

ADD REPLYlink written 22 months ago by rkooliyottil0

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

ADD REPLYlink written 5 weeks ago by g.feng0

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

ADD REPLYlink written 5 weeks ago by genomax59k

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

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by g.feng0

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
ADD REPLYlink written 4 weeks ago by genomax59k

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.

ADD REPLYlink written 4 weeks ago by g.feng0

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

ADD REPLYlink written 4 weeks ago by buchfink100

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
ADD REPLYlink modified 4 weeks ago by genomax59k • written 4 weeks ago by g.feng0

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

ADD REPLYlink written 4 weeks ago by buchfink100

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.

ADD REPLYlink written 5 days ago by g.feng0
2
gravatar for buchfink
22 months ago by
buchfink100
buchfink100 wrote:

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.

ADD COMMENTlink written 22 months ago by buchfink100

Thanks, I am now able to do the process.

ADD REPLYlink written 22 months ago by rkooliyottil0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1471 users visited in the last hour