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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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anvi-compute-genome-similarity exit code ('2') #1336

Closed biotemon closed 4 years ago

biotemon commented 4 years ago

If I try:

anvi-self-test --suite pangenomics

I will get the following output. The error is at the bottom. 


:: Output directory ...

/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output

:: Anvo'o version ...

Anvi'o version ...............................: esther (v6.1-master)
Profile DB version ...........................: 31
Contigs DB version ...........................: 14
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1

:: Setting up the pan analysis directory ...

:: Generating contigs databases for external genomes ...

:: INPUT DIR: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test, FNAME: 01 ...

:: RENAMING CONTIGS ...

Input ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/01.fa
Output .......................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/01-clean.fa
Minimum length ...............................: 0
Total num contigs ............................: 1
Total num nucleotides ........................: 139,930
Contigs removed ..............................: 0 (0.00% of all)
Nucleotides removed ..........................: 0 (0.00% of all)
Deflines simplified ..........................: True

:: GENERATING THE CONTIGS DB ...

Input FASTA file .............................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/01-clean.fa
Name .........................................: 01
Description ..................................: No description is given
Split Length .................................: 20,000                                                                                       
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: None
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: False

Finding ORFs in contigs
===============================================
Genes ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp_0kaapnx/contigs.genes
Amino acid sequences .........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp_0kaapnx/contigs.amino_acid_sequences
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp_0kaapnx/00_log.txt

CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.

Result .......................................: Prodigal (v2.6.2) has identified 119 genes.                                                  

Contigs with at least one gene call ..........: 1 of 1 (100.0%)                                                                              
Contigs database .............................: A new database, /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/01.db, has been created.
Number of contigs ............................: 1
Number of splits .............................: 7
Total number of nucleotides ..................: 139,930
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: True
Desired split length (what the user wanted) ..: 20,000
Average split length (wnat anvi'o gave back) .: 19,990

:: RUNNING HMMs ...

Target found .................................: AA:GENE                                                                                      
Target found .................................: RNA:CONTIG                                                                                   

HMM Profiling for Bacteria_71
===============================================
Reference ....................................: Lee modified, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Bacteria_71/genes.hmm.gz
Number of genes ..............................: 71
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2/00_log.txt
Number of raw hits ...........................: 1                                                                                            

HMM Profiling for Archaea_76
===============================================
Reference ....................................: Lee, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Archaea_76/genes.hmm.gz
Number of genes ..............................: 76
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Archaea_76' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Protista_83
===============================================
Reference ....................................: Delmont, http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Protista_83/genes.hmm.gz
Number of genes ..............................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp515v46x2/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Protista_83' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Ribosomal_RNAs
===============================================
Reference ....................................: Seemann T, https://github.com/tseemann/barrnap
Kind .........................................: Ribosomal_RNAs
Alphabet .....................................: RNA
Context ......................................: CONTIG
Domain .......................................: N\A
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Ribosomal_RNAs/genes.hmm.gz
Number of genes ..............................: 12
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpzwkyhcft
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpzwkyhcft/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Ribosomal_RNAs' returned 0 hits. SAD (but it's stil OK).

:: INPUT DIR: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test, FNAME: 02 ...

:: RENAMING CONTIGS ...

Input ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/02.fa
Output .......................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/02-clean.fa
Minimum length ...............................: 0
Total num contigs ............................: 1
Total num nucleotides ........................: 139,930
Contigs removed ..............................: 0 (0.00% of all)
Nucleotides removed ..........................: 0 (0.00% of all)
Deflines simplified ..........................: True

:: GENERATING THE CONTIGS DB ...

Input FASTA file .............................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/02-clean.fa
Name .........................................: 02
Description ..................................: No description is given
Split Length .................................: 20,000                                                                                       
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: None
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: False

Finding ORFs in contigs
===============================================
Genes ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp82lfcnnz/contigs.genes
Amino acid sequences .........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp82lfcnnz/contigs.amino_acid_sequences
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp82lfcnnz/00_log.txt

CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.

Result .......................................: Prodigal (v2.6.2) has identified 119 genes.                                                  

Contigs with at least one gene call ..........: 1 of 1 (100.0%)                                                                              
Contigs database .............................: A new database, /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/02.db, has been created.
Number of contigs ............................: 1
Number of splits .............................: 7
Total number of nucleotides ..................: 139,930
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: True
Desired split length (what the user wanted) ..: 20,000
Average split length (wnat anvi'o gave back) .: 19,990

:: RUNNING HMMs ...

Target found .................................: AA:GENE                                                                                      
Target found .................................: RNA:CONTIG                                                                                   

HMM Profiling for Bacteria_71
===============================================
Reference ....................................: Lee modified, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Bacteria_71/genes.hmm.gz
Number of genes ..............................: 71
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf/00_log.txt
Number of raw hits ...........................: 1                                                                                            

HMM Profiling for Archaea_76
===============================================
Reference ....................................: Lee, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Archaea_76/genes.hmm.gz
Number of genes ..............................: 76
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Archaea_76' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Protista_83
===============================================
Reference ....................................: Delmont, http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Protista_83/genes.hmm.gz
Number of genes ..............................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp6rwohnjf/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Protista_83' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Ribosomal_RNAs
===============================================
Reference ....................................: Seemann T, https://github.com/tseemann/barrnap
Kind .........................................: Ribosomal_RNAs
Alphabet .....................................: RNA
Context ......................................: CONTIG
Domain .......................................: N\A
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Ribosomal_RNAs/genes.hmm.gz
Number of genes ..............................: 12
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpa2d9mq0a
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpa2d9mq0a/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Ribosomal_RNAs' returned 0 hits. SAD (but it's stil OK).

:: INPUT DIR: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test, FNAME: 03 ...

:: RENAMING CONTIGS ...

Input ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/03.fa
Output .......................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/03-clean.fa
Minimum length ...............................: 0
Total num contigs ............................: 1
Total num nucleotides ........................: 139,930
Contigs removed ..............................: 0 (0.00% of all)
Nucleotides removed ..........................: 0 (0.00% of all)
Deflines simplified ..........................: True

:: GENERATING THE CONTIGS DB ...

Input FASTA file .............................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/03-clean.fa
Name .........................................: 03
Description ..................................: No description is given
Split Length .................................: 20,000                                                                                       
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: None
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: False

Finding ORFs in contigs
===============================================
Genes ........................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpr99hfzo8/contigs.genes
Amino acid sequences .........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpr99hfzo8/contigs.amino_acid_sequences
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpr99hfzo8/00_log.txt

CITATION
===============================================
Anvi'o will use 'prodigal' by Hyatt et al (doi:10.1186/1471-2105-11-119) to
identify open reading frames in your data. When you publish your findings,
please do not forget to properly credit their work.

Result .......................................: Prodigal (v2.6.2) has identified 117 genes.                                                  

Contigs with at least one gene call ..........: 1 of 1 (100.0%)                                                                              
Contigs database .............................: A new database, /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/03.db, has been created.
Number of contigs ............................: 1
Number of splits .............................: 7
Total number of nucleotides ..................: 139,930
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: True
Desired split length (what the user wanted) ..: 20,000
Average split length (wnat anvi'o gave back) .: 19,990

:: RUNNING HMMs ...

Target found .................................: RNA:CONTIG                                                                                   
Target found .................................: AA:GENE                                                                                      

HMM Profiling for Bacteria_71
===============================================
Reference ....................................: Lee modified, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Bacteria_71/genes.hmm.gz
Number of genes ..............................: 71
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il/00_log.txt
Number of raw hits ...........................: 1                                                                                            

HMM Profiling for Archaea_76
===============================================
Reference ....................................: Lee, https://doi.org/10.1093/bioinformatics/btz188
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Archaea_76/genes.hmm.gz
Number of genes ..............................: 76
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Archaea_76' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Protista_83
===============================================
Reference ....................................: Delmont, http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Protista_83/genes.hmm.gz
Number of genes ..............................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp2k4mx7il/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Protista_83' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Ribosomal_RNAs
===============================================
Reference ....................................: Seemann T, https://github.com/tseemann/barrnap
Kind .........................................: Ribosomal_RNAs
Alphabet .....................................: RNA
Context ......................................: CONTIG
Domain .......................................: N\A
HMM model path ...............................: /Users/tito/github/anvio/anvio/data/hmm/Ribosomal_RNAs/genes.hmm.gz
Number of genes ..............................: 12
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp55hpqi2q
Log file .....................................: /var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmp55hpqi2q/00_log.txt
Number of raw hits ...........................: 0                                                                                            

* The HMM source 'Ribosomal_RNAs' returned 0 hits. SAD (but it's stil OK).

:: Importing functions into the contigs database ...

Gene functions ...............................: 494 function calls from 5 sources for 115 unique gene calls has been added to the contigs database.
Gene functions ...............................: 494 function calls from 5 sources for 115 unique gene calls has been added to the contigs database.
Gene functions ...............................: 484 function calls from 5 sources for 113 unique gene calls has been added to the contigs database.

:: Generating an anvi'o genomes storage ...

WARNING
===============================================
Good news! Anvi'o found all these functions that are common to all of your
genomes and will use them for downstream analyses and is very proud of you:
'EGGNOG_BACT, KEGG_PATHWAYS, COG_FUNCTION, COG_CATEGORY, GO_TERMS'.

Internal genomes .............................: 0 have been initialized.                                                                     
External genomes .............................: 3 found.                                                                                     

* g01 is stored with 119 genes (0 of which were partial)
* g02 is stored with 119 genes (0 of which were partial)                                                                                     
* g03 is stored with 117 genes (1 of which were partial)                                                                                     

The new genomes storage ......................: TEST-GENOMES.db (v6, signature: hash536a8295)
Number of genomes ............................: 3 (internal: 0, external: 3)
Number of gene calls .........................: 355
Number of partial gene calls .................: 1

:: Running the pangenome anaysis with default parameters ...

WARNING
===============================================
If you publish results from this workflow, please do not forget to cite DIAMOND
(doi:10.1038/nmeth.3176), unless you use it with --use-ncbi-blast flag, and MCL
(http://micans.org/mcl/ and doi:10.1007/978-1-61779-361-5_15)

Genomes storage ..............................: Initialized (storage hash: hash536a8295)                                                     
Num genomes in storage .......................: 3
Num genomes will be used .....................: 3
Pan database .................................: A new database, /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/TEST-PAN.db, has been created.
Exclude partial gene calls ...................: False

AA sequences FASTA ...........................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/combined-aas.fa

Num AA sequences reported ....................: 355
Num excluded gene calls ......................: 0
Unique AA sequences FASTA ....................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/combined-aas.fa.unique

WARNING
===============================================
You elected to use NCBI's blastp for amino acid sequence search. Running blastp
will be significantly slower than DIAMOND (although, anvi'o developers are
convinced that you *are* doing the right thing, so, kudos to you).

BLAST search db ..............................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/combined-aas.fa.unique
BLAST results ................................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/blast-search-results.txt
Min percent identity .........................: 0.0                                                                                          
Minbit .......................................: 0.5
Filtered search results ......................: 1,053 edges stored                                                                           
MCL input ....................................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/mcl-input.txt
MCL inflation ................................: 2.0
MCL output ...................................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/mcl-clusters.txt
Number of gene clusters ......................: 121

CITATION
===============================================
Anvi'o will use 'muscle' by Edgar, doi:10.1093/nar/gkh340
(http://www.drive5.com/muscle) to align your sequences. If you publish your
findings, please do not forget to properly credit their work.

New data for 'items' in data group 'default'
===============================================
Data key "num_genomes_gene_cluster_has_hits" .: Predicted type: int
Data key "num_genes_in_gene_cluster" .........: Predicted type: int
Data key "max_num_paralogs" ..................: Predicted type: int
Data key "SCG" ...............................: Predicted type: int

WARNING
===============================================
You (or the programmer) asked anvi'o to NOT check the consistency of the names
of your items between your additional data and the pan database you are
attempting to update. So be it. Anvi'o will not check anything, but if things
don't look the way you expected them to look, you will not blame anvi'o for your
poorly prepared data, but choose between yourself or Obama.

NEW DATA
===============================================
Database .....................................: pan
Data group ...................................: default
Data table ...................................: items
New data keys ................................: num_genomes_gene_cluster_has_hits, num_genes_in_gene_cluster, max_num_paralogs, SCG.

gene clusters info ...........................: 121 gene_clusters stored in the database                                                     
New items order ..............................: "frequency:euclidean:ward" (type newick) has been added to the database...                   

WARNING
===============================================
Clustering for "frequency:euclidean:ward" is already in the database. It will be
replaced with the new content.

New items order ..............................: "frequency:euclidean:ward" (type newick) has been added to the database...
New items order ..............................: "presence-absence:euclidean:ward" (type newick) has been added to the database...            
New items order ..............................: "Forced synteny <> g01:NA:NA" (type basic) has been added to the database...
New items order ..............................: "Forced synteny <> g02:NA:NA" (type basic) has been added to the database...
New items order ..............................: "Forced synteny <> g03:NA:NA" (type basic) has been added to the database...

New layer_orders data...
===============================================
Data key "gene_cluster presence absence" .....: Type: newick
Data key "gene_cluster frequencies" ..........: Type: newick

New order data added to the db for layer_orders : gene_cluster presence absence, gene_cluster frequencies.

New data for 'layers' in data group 'default'
===============================================
Data key "total_length" ......................: Predicted type: int
Data key "gc_content" ........................: Predicted type: float
Data key "percent_completion" ................: Predicted type: int
Data key "percent_redundancy" ................: Predicted type: int
Data key "num_genes" .........................: Predicted type: int
Data key "avg_gene_length" ...................: Predicted type: float
Data key "num_genes_per_kb" ..................: Predicted type: float
Data key "singleton_gene_clusters" ...........: Predicted type: int
Data key "num_gene_clusters" .................: Predicted type: int

NEW DATA
===============================================
Database .....................................: pan
Data group ...................................: default
Data table ...................................: layers
New data keys ................................: total_length, gc_content, percent_completion, percent_redundancy, num_genes, avg_gene_length, num_genes_per_kb, singleton_gene_clusters, num_gene_clusters.

Genomes storage .............................................: Initialized (storage hash: hash536a8295)                                      
Num genomes in storage ......................................: 3
Num genomes will be used ....................................: 3
Pan DB ......................................................: Initialized: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/TEST-PAN.db (v. 13)
Gene cluster homogeneity estimates ..........................: Functional: [NO]; Geometric: [NO]; Combined: [NO]

* Gene clusters are initialized for all 121 gene clusters in the database.

New data for 'items' in data group 'default'
===============================================
Data key "functional_homogeneity_index" ......: Predicted type: float
Data key "geometric_homogeneity_index" .......: Predicted type: float
Data key "combined_homogeneity_index" ........: Predicted type: float

WARNING
===============================================
You (or the programmer) asked anvi'o to NOT check the consistency of the names
of your items between your additional data and the pan database you are
attempting to update. So be it. Anvi'o will not check anything, but if things
don't look the way you expected them to look, you will not blame anvi'o for your
poorly prepared data, but choose between yourself or Obama.

NEW DATA
===============================================
Database .....................................: pan
Data group ...................................: default
Data table ...................................: items
New data keys ................................: functional_homogeneity_index, geometric_homogeneity_index, combined_homogeneity_index.

log file ....................................................: /private/var/folders/86/v68d1x9s59128vx4pr1kls6r0000gn/T/tmpt_mes0n4/test-output/pan_test/TEST/log.txt

:: Running ANI on genomes and storing results in the PAN database ...

usage: anvi-compute-genome-similarity [-h] [-i FILE_PATH] [-e FILE_PATH]
                                      [-f FASTA_TEXT_FILE] -o DIR_PATH
                                      [-p PAN_DB] --program
                                      {pyANI,fastANI,sourmash}
                                      [--fastani-kmer-size FASTANI_KMER_SIZE]
                                      [--fragment-length FRAGMENT_LENGTH]
                                      [--min-num-fragments MIN_NUM_FRAGMENTS]
                                      [--method {ANIm,ANIb,ANIblastall,TETRA}]
                                      [--min-alignment-fraction NUM]
                                      [--significant-alignment-length INT]
                                      [--min-full-percent-identity FULL_PERCENT_IDENTITY]
                                      [--kmer-size INT] [--scale INT]
                                      [--distance DISTANCE_METRIC]
                                      [--linkage LINKAGE_METHOD]
                                      [-T NUM_THREADS] [--just-do-it]
                                      [--log-file FILE_PATH]
anvi-compute-genome-similarity: error: the following arguments are required: --program

Config Error: According to the exit code ('2'), anvi'o suspects that something may have gone
              wrong while running your tests :/ We hope that the reason is clear to you from
              the lines above. But if you don't see anything obvious, and especially if the 
              test ended up running until the end with reasonable looking final results, you
              shouldn't worry too much about this error. Life is short and we all can worry 
              just a bit less.

This test was run on a iMac (macOS Mojave Version 10.14.6)

I followed master installation mentioned in http://merenlab.org/2016/06/26/installation-v2/#following-the-active-codebase-youre-a-wizard-arry I also installed muscle http://merenlab.org/2016/06/18/installing-third-party-software/#muscle

Thank you for your input on how to solve this issue.

Thank you.

meren commented 4 years ago

This is now fixed, Tito. Please try again after a git pull :)