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Hello there,
I don't seem to be able to get a .dnd output when running mashtree from *msh files, whereas I can get a .dnd output if I run mashtree using the fastq files as input... see below
I ran mashtree --mindepth 0 --numcpus 4 --outmatrix mashmatrix.txt ERR*/*msh > mashtree.dnd
on the output generated by mash sketch -k 21 -s 10000 - -o ${out_dir}"/"${id}
with the following log
mashtree: main: Found mash version 2 - /home/xxx/.local/bin/mash
mashtree: main: Temporary directory will be /tmp/xxx_16154334/MASHTREE.EUJ6ti
mashtree: main: mashtree on 448 files
mashtree: mashSketch(TID2): This thread will work on 112 sketches
mashtree: mashSketch(TID2): Working on file 1 out of 112
mashtree: mashSketch(TID2): Input file is a sketch file itself and will be used as such: ERRxxx/ERRxxx.msh
mashtree: mashSketch(TID2): WARNING: ERRxxx.msh was already mashed.
.....
mashtree: mashDist(TID6): Distances for /tmp/xxx_16154334/MASHTREE.EUJ6ti/ERRxxx1.msh
mashtree: mashDist(TID7): Distances for /tmp/xxx_16154334/MASHTREE.EUJ6ti/ERRxxx2.msh
mashtree: mashDist(TID5): Distances for /tmp/xxx_16154334/MASHTREE.EUJ6ti/ERRxxx3.msh
mashtree: mashDist(TID6): Distances for /tmp/xxx_16154334/MASHTREE.EUJ6ti/ERRxxx4.msh
mashtree: mashDist(TID5): Distances for /tmp/xxx_16154334/MASHTREE.EUJ6ti/ERRxxx5.msh
mashtree: mashDistance: Databasing distances (1/4, TID5)
mashtree: mashDistance: Waiting to join thread (2/4, TID6)
mashtree: mashDistance: Databasing distances (2/4, TID6)
mashtree: mashDistance: Waiting to join thread (3/4, TID7)
mashtree: mashDistance: Databasing distances (3/4, TID7)
mashtree: mashDistance: Waiting to join thread (4/4, TID8)
mashtree: mashDistance: Databasing distances (4/4, TID8)
mashtree: mashDistance: Converting to phylip format into /tmp/xxxx_16154334/MASHTREE.EUJ6ti/distances.phylip
mashtree: mashDistance: Writing a distance matrix to mashmatrix.txt
mashtree: Mashtree::createTreeFromPhylip: Can't call method "as_text" on an undefined value
Stopped at ...Mashtree.pm line 339.
the outmatrix was generated, but not the .dnd output...
looking at Mashtree.pm it seems that $outdir/tree.dnd.tmp was not created ( I removed unlink() on line 343 but no .tmp file appeared).
Mashtree version 1.4.6, installed with conda on a Linux cluster with the following configuration 4.18.0-513.9.1.el8_9.x86_64
could not install via cpanm because of some missing dependencies that I could not install without sudo.
now if I run cpanm -l ~ Mashtree I get Mashtree is up to date. (1.4.6)
Is it advisable to use fastq rather than msh as input? Many thanks!
The text was updated successfully, but these errors were encountered:
Sorry for the hitchhiking... I have the exact same error message when trying to run mashtree (1.4.6) with *.msh files as input.
looking at Mashtree.pm it seems that $outdir/tree.dnd.tmp was not created
It seems like the issue is with distancesToPhylip because the distances.phylip file is almost empty (in my case) - I guess it should have the matrix of distances in PHYLIP format so that quicktree can draw trees in the next step:
$ cat temp_mashtree/distances.phylip
0
I wonder if the issue is when trying to parse the genome names to create the phylip distance matrix. In my case, the first several lines of the distances.db.tsv file looks like this:
Is there a rule the genome file names need to follow (limit in length, etc.)?
...
[Edit:] When I tried the same set with the fasta sequence files as input, mashtree ran successfully. It would be good to be able to work with msh files as well, though.
Hello there,
I don't seem to be able to get a .dnd output when running mashtree from *msh files, whereas I can get a .dnd output if I run mashtree using the fastq files as input... see below
I ran
mashtree --mindepth 0 --numcpus 4 --outmatrix mashmatrix.txt ERR*/*msh > mashtree.dnd
on the output generated by
mash sketch -k 21 -s 10000 - -o ${out_dir}"/"${id}
with the following log
the outmatrix was generated, but not the .dnd output...
looking at Mashtree.pm it seems that $outdir/tree.dnd.tmp was not created ( I removed unlink() on line 343 but no .tmp file appeared).
Mashtree version 1.4.6, installed with conda on a Linux cluster with the following configuration 4.18.0-513.9.1.el8_9.x86_64
could not install via cpanm because of some missing dependencies that I could not install without sudo.
now if I run
cpanm -l ~ Mashtree
I getMashtree is up to date. (1.4.6)
Is it advisable to use fastq rather than msh as input? Many thanks!
The text was updated successfully, but these errors were encountered: