# Running time during mapping with diamond

**URL:** <https://forum.biobakery.org/t/running-time-during-mapping-with-diamond/4250>\
**Category:** PhyloPhlAn\
**Created:** [October 16, 2022, 11:03pm UTC](https://forum.biobakery.org/t/running-time-during-mapping-with-diamond/4250 "2022-10-16T23:03:14Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Joel\_Sanchez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/joel_sanchez/32/1727_2.png) [@Joel\_Sanchez](https://forum.biobakery.org/u/Joel_Sanchez)\
**Post date:** [October 16, 2022, 11:03pm UTC](https://forum.biobakery.org/t/running-time-during-mapping-with-diamond/4250/1 "2022-10-16T23:03:14Z")

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Hi developers,

I would like to know if I am making a mistake that make the mapping a very slow process. After 24h, I killed the process because only one genome has been mapped.

**My code:**  
phylophlan\_write\_config\_file -o supermatrix\_aa.cfg -d a --force\_nucleotides --db\_aa diamond --map\_dna diamond --map\_aa diamond --msa muscle --trim trimal --tree1 fasttree --tree2 raxml

phylophlan -i Syn\_genomes -o output\_Syn\_genomes -d phylophlan -t a -f supermatrix\_aa.cfg --diversity low --force\_nucleotides --nproc 4 --verbose 2\>&1 | tee phylophlan\_output/phylophlan\_out.log

**Log\_output\_info:** :  
apping “output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna”  
“CB0205-GCA\_000179255.1.b6o.bkp” generated in 1248s  
Removing “output\_Syn\_genomes/tmp/map\_dna/LA31-GCA\_018502385.1.b6o.bkp”

[e] Command ‘[’/opt/anaconda3/envs/phylophlan/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query-gencode’, ‘11’, ‘–query’, ‘output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna’, ‘–db’, ‘phylophlan\_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘output\_Syn\_genomes/tmp/map\_dna/LA31-GCA\_018502385.1.b6o.bkp’]’ died with \<Signals.SIGKILL: 9\>.

[e] cannot execute command  
command\_line: /opt/anaconda3/envs/phylophlan/bin/diamond blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query-gencode 11 --query output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna --db phylophlan\_databases/phylophlan/phylophlan.dmnd --out output\_Syn\_genomes/tmp/map\_dna/LA31-GCA\_018502385.1.b6o.bkp  
stdin: None  
stdout: None  
env: {‘TERM\_PROGRAM’: ‘Apple\_Terminal’, ‘SHELL’: ‘/bin/zsh’, ‘TERM’: ‘xterm-256color’, ‘TMPDIR’: ‘/var/folders/z6/2b8qw16n2fd5hg1jrhf358z80000gn/T/’, ‘CONDA\_SHLVL’: ‘2’, ‘CONDA\_PROMPT\_MODIFIER’: '(phylophlan) ', ‘TERM\_PROGRAM\_VERSION’: ‘444’, ‘TERM\_SESSION\_ID’: ‘77A99F7E-2B2E-40EB-A839-24F84EC424BC’, ‘USER’: ‘joelsanchez’, ‘CONDA\_EXE’: ‘/opt/anaconda3/bin/conda’, ‘SSH\_AUTH\_SOCK’: ‘/private/tmp/com.apple.launchd.P2Ejd0CSjE/Listeners’, ‘_CE\_CONDA’: ‘’, ‘CONDA\_PREFIX\_1’: ‘/opt/anaconda3’, ‘PATH’: ‘/opt/anaconda3/envs/phylophlan/bin:/opt/anaconda3/condabin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/ncbi/blast/bin:/opt/X11/bin’, '_’: ‘/opt/anaconda3/envs/phylophlan/bin/phylophlan’, ‘CONDA\_PREFIX’: ‘/opt/anaconda3/envs/phylophlan’, ‘\_\_CFBundleIdentifier’: ‘com.apple.Terminal’, ‘PWD’: ‘/Users/joelsanchez/phylophlan/phylophlan’, ‘LANG’: ‘en\_US.UTF-8’, ‘XPC\_FLAGS’: ‘0x0’, ‘\_CE\_M’: ‘’, ‘XPC\_SERVICE\_NAME’: ‘0’, ‘SHLVL’: ‘1’, ‘HOME’: ‘/Users/joelsanchez’, ‘CONDA\_PYTHON\_EXE’: ‘/opt/anaconda3/bin/python’, ‘LOGNAME’: ‘joelsanchez’, ‘CONDA\_DEFAULT\_ENV’: ‘phylophlan’, ‘\_\_CF\_USER\_TEXT\_ENCODING’: ‘0x1F5:0x0:0x0’}

[e] Command ‘[’/opt/anaconda3/envs/phylophlan/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query-gencode’, ‘11’, ‘–query’, ‘output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna’, ‘–db’, ‘phylophlan\_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘output\_Syn\_genomes/tmp/map\_dna/LA31-GCA\_018502385.1.b6o.bkp’]’ died with \<Signals.SIGKILL: 9\>.

[e] error while mapping  
{‘program\_name’: ‘/opt/anaconda3/envs/phylophlan/bin/diamond’, ‘params’: ‘blastx --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query-gencode 11’, ‘input’: ‘–query’, ‘database’: ‘–db’, ‘output’: ‘–out’, ‘version’: ‘version’, ‘command\_line’: ‘#program\_name# #params# #input# #database# #output#’}  
output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna  
phylophlan\_databases/phylophlan/phylophlan.dmnd  
output\_Syn\_genomes/tmp/map\_dna  
LA31-GCA\_018502385.1.b6o.bkp  
True

[e] Command ‘[’/opt/anaconda3/envs/phylophlan/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query-gencode’, ‘11’, ‘–query’, ‘output\_Syn\_genomes/tmp/clean\_dna/LA31-GCA\_018502385.1.fna’, ‘–db’, ‘phylophlan\_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘output\_Syn\_genomes/tmp/map\_dna/LA31-GCA\_018502385.1.b6o.bkp’]’ died with \<Signals.SIGKILL: 9\>.

[e] gene\_markers\_identification crashed

Thanks,

Joel

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**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [November 18, 2022, 4:06pm UTC](https://forum.biobakery.org/t/running-time-during-mapping-with-diamond/4250/2 "2022-11-18T16:06:34Z")

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Hi Joel,

Thanks for writing to us. So, the slowness could be due to the diamond version. Version 2 is actually much slower than version 1 because a bug was fixed, you can read more about it here: [Announcing HUMAnN 3.6 (Critical Update)](https://forum.biobakery.org/t/announcing-humann-3-6-critical-update/4155).

From the log it seems that one genome was mapped in ~20m, right? But the error after that is due to you killing PhyloPhlAn because too slow?  
Also, you’re specifying 4 cores, which means 4 input genomes will be mapped at the same time, to speed up the process you can specify more (if you can) so that more genomes will be mapped in the same amount of time.

Thanks a lot,  
Francesco