DIAMOND v2.0.15

[bbuchfink]

• Fixed a bug (present since v2.0.12) that caused the diamond view workflow to report a zero bit score for all alignments.

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This discussion was created from the release DIAMOND v2.0.15.

[amrhemeda]

How I can download this on MacBook? I need version for my macbook

[bbuchfink]

You can try to download using bioconda, homebrew or compiling from source.

[jedsoncardoso]

/data/database/diamond/src/output/daa/daa_write.cpp: In function ‘void finish_daa(OutputFile&, DAA_file&, const StringSet&, const std::vector&, int64_t)’:
/data/database/diamond/src/output/daa/daa_write.cpp:146:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int64_t i = 0; i < seq_ids.size(); ++i) {

[jedsoncardoso]

When performing analysis using NR NCBI database, it takes a long time to write DAA file, my dataset has 1162522 reads only. My server has 80 threads and 1TB of RAM. However, before to DIAMOND v2.0.15., it was performed in 12 hours. I think that new version has some error?

[bbuchfink]

When performing analysis using NR NCBI database, it takes a long time to write DAA file, my dataset has 1162522 reads only. My server has 80 threads and 1TB of RAM. However, before to DIAMOND v2.0.15., it was performed in 12 hours. I think that new version has some error?

I tested this and didn't see a performance problem writing DAA files. Please let me know the nature of your input data and your command line parameters.

[jedsoncardoso]

#diamond v2.0.15.153
#Sample are Paired-end Reads
diamond blastx -d nr_x86 -p $4 -q Sample_merged.fastq -o Sample_merged_nr_diamond -t Sample_temp_dir -f 100 -k 1 -b 18 -c 1 --salltitles -e 0.0001 --unal 1 --un Sample_merged_nr_diamond_unaligned

[jedsoncardoso]

#diamond v2.0.15.153
#Sample are Paired-end Reads
diamond blastx -d nr_x86 -p 80 -q Sample_merged.fastq -o Sample_merged_nr_diamond -t Sample_temp_dir -f 100 -k 1 -b 18 -c 1 --salltitles -e 0.0001 --unal 1 --un Sample_merged_nr_diamond_unaligned

[jedsoncardoso]

Dear,
I downgraded Diamond to v2.0.11.149, re-indexed NCBI
NR Database. Then, I performed the analysis of the 1,160,907 reads again.

This script started at Tue Oct 4 19:04:23 -03 2022
This script finished at Wed Oct 5 02:14:02 -03 2022

DIAMOND_DB=/data/database/DiamondDB

/opt/02_Alignment/diamond/bin/diamond blastx -d $DIAMOND_DB/nr_x86 -p 40 -q Sample_merged.fastq -o Sample_merged_nr_diamond -t Sample_temp_dir -f 100 -k 1 -b 18 -c 1 --salltitles -e 0.0001 --unal 1 --un Sample_merged_nr_diamond_unaligned

[learnitXD]

After downloading the Windows.zip which has the diamond application,
I double clicked , then select run or install, but no windows came up.
How can I install Diamond to Windows 11?

[bbuchfink]

You need to run diamond from the command prompt.

[wandersonlimacunha1]

This didn't work for me, start using "start diamond.exe", and it just disappeared

[DrSHI2024]

I just encountered the same problem in windows11.

[bbuchfink]

Using start is not correct. You just need to open the command prompt and run diamond.