error in HUManN2 analysis of PiCrust data (could not convert string to float)

[jb2...@gmail.com]

Hi HUMAnN group:

I am trying to analyze PiCrust output with HUManN2. I took the PiCrust Biom file and I first split the table to make individual Biom files for each of my samples. I then tried the following command on that .biom file:

csmxum00009464:humann2 jennifer.bowen$ humann2 --input /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann2_try/GULF.9B.RNA.biom output humann_out pathways-database /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/data/keggc

The output message I received is below. I have been following the instructions from this site:
http://huttenhower.sph.harvard.edu/humann2/manual#markdown-header-1-download-humann2

Since the output files are straight out of PiCrust, I am not sure how to solve the problem. I would be grateful for any suggestions.

Best regards,
Jen

usage: humann2 [-h] [--version] [-v] [-r] [--bypass-prescreen]
[--bypass-nucleotide-index] [--bypass-translated-search]
[--bypass-nucleotide-search] -i <input.fastq> -o <output>
[--nucleotide-database <nucleotide_database>]
[--annotation-gene-index <8>]
[--protein-database <protein_database>] [--evalue <1.0>]
[--metaphlan <metaphlan>]
[--metaphlan-options <metaphlan_options>]
[--o-log <sample.log>]
[--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
[--remove-temp-output] [--bowtie2 <bowtie2>] [--threads <1>]
[--prescreen-threshold <0.01>] [--identity-threshold <40.0>]
[--usearch <usearch>] [--rapsearch <rapsearch>]
[--diamond <diamond>]
[--taxonomic-profile <taxonomic_profile.tsv>]
[--id-mapping <id_mapping.tsv>]
[--translated-alignment {usearch,rapsearch,diamond}]
[--xipe {on,off}] [--minpath {on,off}] [--pick-frames {on,off}]
[--output-format {tsv,biom}] [--output-max-decimals <10>]
[--output-basename <sample_name>] [--remove-stratified-output]
[--input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}]
[--pathways-database <pathways_database.tsv>]
[--pathways {metacyc,unipathway}]
[--memory-use {minimum,maximum}]
humann2: error: argument -o/--output is required
csmxum00009464:humann2 jennifer.bowen$ humann2 --input /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann2_try/GULF.9B.RNA.biom --output humann_out --pathways-database /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/data/keggc
Creating output directory: /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out
Output files will be written to: /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out

Process the gene table ...

Computing pathways abundance and coverage ...
Traceback (most recent call last):
File "/Users/jennifer.bowen/anaconda/lib/python2.7/site-packages/humann2-0.5.0-py2.7.egg/humann2/quantify/MinPath12hmp.py", line 927, in <module>
Orth2Path(infile = anyfile, mpsfile = mpsfile, reportfile = reportfile, detailfile = detailfile, whichdb = "ANY", mapfile=mapfile)
File "/Users/jennifer.bowen/anaconda/lib/python2.7/site-packages/humann2-0.5.0-py2.7.egg/humann2/quantify/MinPath12hmp.py", line 874, in Orth2Path
ab = float(tmp[1])
ValueError: could not convert string to float: cycle

CRITICAL ERROR: Unable to process all thread commands.

Error message returned from command for thread task 0: /Users/jennifer.bowen/anaconda/bin/python /Users/jennifer.bowen/anaconda/lib/python2.7/site-packages/humann2-0.5.0-py2.7.egg/humann2/quantify/MinPath12hmp.py -any /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out/GULF.9B.RNA_humann2_temp/tmpxvkWTu/tmp7vK2D5 -map /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out/GULF.9B.RNA_humann2_temp/tmpxvkWTu/tmpmP9BFc -report /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out/GULF.9B.RNA_humann2_temp/tmpxvkWTu/tmp6Zpfln -details /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out/GULF.9B.RNA_humann2_temp/tmpxvkWTu/tmp8V6piX -mps /Users/jennifer.bowen/Desktop/humann2_v0.5.0/humann2/humann_out/GULF.9B.RNA_humann2_temp/tmpxvkWTu/tmpNOLdsu

[Lauren McIver]

Hello Jen,

It looks like the input file has an unexpected format. Is the input file the split output file from predict_metagenomes.py or metagenome_contributions.py from PICRUSt version 1.0.0-devel? It looks like from your error message the file might have some unexpected fields (ie instead of all KOs it appears there might be a pathway name). 

Thank you,

Lauren

[Jennifer Bowen]

YES!  I had the later .biom file.  Just tried it with the former and it worked great.  THANK YOU!

Jennifer Bowen
Associate Professor
Biology Department 
University of Massachusetts Boston
jennife...@umb.edu
617.287.6626