diamond Error: Inflate error

shashikanth

New member
Hi,

im trying to analyze my nanopore metagenomic data on 15 GB RAM AWS Server using diamond tool.
The command i used for making database is
diamond makedb --in nr.gz -d diamondDB/ --taxonmap prot.accession2taxid.gz --taxonnodes taxdmp.zip -p 96
after processing for 1 hour the execution stops with Error: Inflate error. even after trying multiple times.
If any one helps me to resolve this issue.

Thank you
 

Benjamin Buchfink

Administrator
Staff member
This indicates an error in the input file. Try to test the integrity of the file like this:
gzip -tv nr.gz

If that shows an error, try to download the file again.

Also, the parameter of the --taxonnodes option needs to be the nodes.dmp file contained in the taxdmp.zip file, not that file itself.
 

shashikanth

New member
This indicates an error in the input file. Try to test the integrity of the file like this:
gzip -tv nr.gz

If that shows an error, try to download the file again.

Also, the parameter of the --taxonnodes option needs to be the nodes.dmp file contained in the taxdmp.zip file, not that file itself.
Thank you so much for replying i will try to correct them check if its working
 

shashikanth

New member
i have tried gzip -tv nr.gz
it gives nr.gz:
and just stops there
i will try again downloding nr.gz file and do the analysis
 

shashikanth

New member
Hi,

im trying to analyze my nanopore metagenomic data on 15 GB RAM AWS Server using diamond tool.
The command i used for making database is
diamond makedb --in nr.gz -d diamondDB/ --taxonmap prot.accession2taxid.gz --taxonnodes taxdmp.zip -p 96
after processing for 1 hour the execution stops with Error: Inflate error. even after trying multiple times.
If any one helps me to resolve this issue.

Thank you
HI i have tried downloading the new nr.gz file and did analysis. know it shows RAM problems
i have 15 GB RAM
how to resolve this issue.
 

shashikanth

New member
Error: Invalid option: --block-size/-b. Block size is set for the alignment commands.

if i use -b in the command it shows this error
any other suggestions please
 

Ewelina

New member
I am getting the same error: Inflate error.

So far, I have built the diamond database successfully. (at least so I think?)

wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.gz
wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
unzip taxdmp.zip -d taxdmp
gunzip nr.gz
gunzip prot.accession2taxid.gz
diamond makedb --in nr -d diamondnr --taxonmap prot.accession2taxid --taxonnodes taxdmp


I am getting stuck here -- when I try to run the actual blastp command

diamond blastp -d diamondnr -q Om-4483-DE-pep.fasta -o Om-diamond --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids --taxonmap prot.accession2taxid --taxonnodes taxdmp/nodes.dmp

Here is what I get in response:

diamond v0.9.12.113 | by Benjamin Buchfink <buchfink@gmail.com>
Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.
#CPU threads: 24
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
#Target sequences to report alignments for: 25
Temporary directory:
Opening the database... [0.008753s]
Loading taxonomy... [0.012191s]
Error: Inflate error.

What am I missing? is there any other required parameter that I should be passing?
 

Benjamin Buchfink

Administrator
Staff member
Please try to use the latest version of Diamond. It has the advantage that you only need to pass --taxonmap and --taxonnodes to the makedb command and it will be built into the database. Also, you don't need to decompress the nr.gz and prot.accession2taxid.gz files, Diamond can handle the compressed files.
 
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