Metameta fails with example file

tadKeys commented 6 years ago

Hi,

I tested metameta now with an example file, and it also fails at the metameta step:

run.sh

metameta --configfile test.yaml --use-conda --keep-going --cores 5

*) test.yaml

workdir: "/home/stephan/work/10_meta_meta/output/"
dbdir: "/home/stephan/work/01_meta_meta_db/"

samples:
  "sample1":
    fq1: "/home/stephan/work/miniconda/data/opt/metameta/sampledata/files/reads/sample_data_archaea_bacteria.1.fq.gz"

databases:
  - archaea_bacteria_201503
tools:
    "clark": "p"
    "kaiju": "p"

threads: 30
gzipped: 1
keepfiles: 1

metametamerge.log
```
   MetaMetaMerge 1.1
```
Input files: clark (p) sample1/profiles/archaea_bacteria_201503/clark.profile.out /home/stephan/work/01_meta_meta_db/archaea_bacteria_201503/clark.dbprofile.out kaiju (p) sample1/profiles/archaea_bacteria_201503/kaiju.profile.out /home/stephan/work/01_meta_meta_db/archaea_bacteria_201503/kaiju.dbprofile.out Taxonomy: /home/stephan/work/01_meta_meta_db/taxonomy/names.dmp, /home/stephan/work/01_meta_meta_db/taxonomy/nodes.dmp, /home/stephan/work/01_meta_meta_db/taxonomy/merged.dmp Bins: 4 Cutoff: 0.0001 Mode: linear Ranks: species Output file (type): sample1/metametamerge/archaea_bacteria_201503/final.metametamerge.profile.out (bioboxes) Verbose: False Detailed: False

Parsing taxonomy (names, nodes, merged) ...

Reading database profiles ...

/home/stephan/work/01_meta_meta_db/archaea_bacteria_201503/clark.dbprofile.out (tsv) species - 1461 entries (0 ignored) 2 taxons with merged entries [94694,1905730] Total - 1459 taxons
/home/stephan/work/01_meta_meta_db/archaea_bacteria_201503/kaiju.dbprofile.out (tsv) species - 2419 entries (0 ignored) 4 taxons with merged entries [1405,94694,1334193,1905730] Total - 2415 taxons

Reading profiles ...

sample1/profiles/archaea_bacteria_201503/clark.profile.out (tsv) species - 0 entries (0 ignored) (WARNING) no valid entries found [species] Traceback (most recent call last): File "/mnt/vdb1/stephan/10_meta_meta/output/.snakemake/conda/266fca67/bin/MetaMetaMerge.py", line 338, in main() File "/mnt/vdb1/stephan/10_meta_meta/output/.snakemake/conda/266fca67/bin/MetaMetaMerge.py", line 131, in main tool = Tools(input_file, identifiers[idx], methods[idx], parse_files(input_file, methods[idx], all_names_scientific, all_names_other, nodes, merged, ranks, args.verbose), ranks, args.verbose) File "/mnt/vdb1/stephan/10_meta_meta/output/.snakemake/conda/266fca67/lib/python3.5/site-packages/metametamerge/Tools.py", line 11, in init Profile.init(self, profile, ranks) File "/mnt/vdb1/stephan/10_metameta/output/.snakemake/conda/266fca67/lib/python3.5/site-packages/metametamerge/Profile.py", line 15, in init self.profilerank[rankid] = ProfileRank(profile[np.ix(profile[:,1]==rankid, [0,2,3])],rankid,sum(profile[:,1]==rankid)) IndexError: too many indices for array



Thanks for your help in advance,
Stephan

tadKeys commented 6 years ago

I think I found the error - it's probably misuse of binning and profiling

tools:
    "clark": "p"  <-- here
    "kaiju": "p"

Best, Stephan

pirovc commented 6 years ago

Hi Stephan,

Very probably that's the cause, because the sample data should produce meaningful results. Keep it in mind that if some tool does not have results, meaning the reads didn't match anywhere in the db, such error will still occur. That will be fixed on the v1.2.2.

Best. Vitor

tadKeys commented 6 years ago

Hi Vitor,

just wanted to let you know that the run completed.

Thanks and looking forward to the updates, Stephan

pirovc / metameta

Metameta fails with example file #14