error during Mapping "phylophlan"

[Jiffin Paulose]

Hi again.  I've abandoned the idea of running this on my University's cluster, so I've set it up at home on my Ubuntu desktop (32gb RAM, 8-core AMD processor).  Everything works as far as config checking, etc.  When running the example list provided or any dataset, I get the following error after the "Checking" and "Cleaning" steps for all of the .faa files:

Mapping "output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa"

[e] cannot remove "", file not found

[e] Command '['diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp']' returned non-zero exit status 1

[e] cannot execute command

    command_line: diamond blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa --db phylophlan_databases/phylophlan/phylophlan.dmnd --out output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp

           stdin: None

          stdout: None

             env: None

[e] Command '['diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp']' returned non-zero exit status 1

[e] error while mapping

    {'command_line': '#program_name# #params# #input# #database# #output#', 'output': '--out', 'input': '--query', 'database': '--db', 'params': 'blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0', 'program_name': 'diamond', 'version': 'version'}

    output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa

    phylophlan_databases/phylophlan/phylophlan.dmnd

    output/example_corynebacteria_phylophlan/tmp/map_aa

    C_glucuronolyticum_ATCC51866.b6o.bkp

    1

    True

[e] Command '['diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp']' returned non-zero exit status 1

[e] gene_markers_identification crashed

The command is:

python phylophlan2.py -i input/example_corynebacteria -d phylophlan -f supertree_aa.cfg -t a --diversity medium --fast --output_folder output --verbose

The config file is the one generated by the default_configs script.

[Francesco Asnicar]

Hi,

I'm looking into this issue, in the meantime it would be helpful if you can run and provide the output of the command posted in the error output (I removed the --quite param so we can get more info from diamond), to see what error it generates:

diamond blastp --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa --db phylophlan_databases/phylophlan/phylophlan.dmnd --out output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp

Many thanks,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/06e22d9a-cab4-4619-9583-3bcc44bd9f7b%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jiffin Paulose]

Hi Francesco,

Thanks for looking into this:

(ppa2) jiffin@jpwinbuntu:~/phylophlan$ diamond blastp --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query output/example_corynebacteria_phylophlan/tmp/clean_aa/C_glucuronolyticum_ATCC51866.faa --db phylophlan_databases/phylophlan/phylophlan.dmnd --out output/example_corynebacteria_phylophlan/tmp/map_aa/C_glucuronolyticum_ATCC51866.b6o.bkp
diamond v0.9.22.123 | by Benjamin Buchfink <buch...@gmail.com>
Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

#CPU threads: 1
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: output/example_corynebacteria_phylophlan/tmp/map_aaOpening the database... [0.003246s]
Error: Database file is not a DIAMOND database.

[Francesco Asnicar]

Thanks for the quick reply!

Apparently something went wrong when building the database... Can you please forward the config file (or just post the "db_aa" section)?

Also, can you please provide the file info of "phylophlan.dmnd":
$ ls -l phylophlan_databases/phylophlan/phylophlan.dmnd

Many thanks,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/64162a95-2825-47e8-ae06-382eb526f2b1%40googlegroups.com.

[Jiffin Paulose]

[db_aa]
program_name = diamond
params = makedb
threads = --threads
input = --in
output = --db
version = version
command_line = #program_name# #params# #threads# #input# #output#

jiffin@jpwinbuntu:~/phylophlan$ ls -l phylophlan_databases/phylophlan/phylophlan.dmnd
-rw-rw-r-- 1 jiffin jiffin 0 Nov 1 20:31 phylophlan_databases/phylophlan/phylophlan.dmnd

[Francesco Asnicar]

Many thanks!

The configuration looks good, and the problem is that the diamond database file is 0 in size... most likely something went wrong when building the PhyloPhlAn database (not sure what or why, though, given the config looks ok).

I would suggest removing the "phylophlan_databases/phylophlan" folder, but before running PhyloPhlAn we should check that the other files are ok too.

In the "phylophlan_databases" folder, you should have:

  * "phylophlan.tar" of 68M (ls -l --> 70758400)

  * "phylophlan.md5" of 49 bytes (ls -l --> 49)

If the two phylophlan.* files you have in "phylophlan_databases" do not match with the above sizes, please remove them so that PhyloPhlAn will download them again.

So, after having removed/checked the database files, if you run PhyloPhlAn again, it should rebuild the database and hopefully this time the "phylophlan_databases/phylophlan/phylophlan.dmnd" diamond database won't have a size of 0.

Many thanks,

Francesco

--
You received this message because you are subscribed to the Google Groups "PhyloPhlAn-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to phylophlan-use...@googlegroups.com.
To post to this group, send email to phylophl...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/phylophlan-users/a7893361-ad06-471e-ad39-389964d1cf79%40googlegroups.com.

[Jiffin Paulose]

Francesco, it appears to be working!  I'm running through a dataset right now, I'll keep you updated.  Many thanks, again!!