anvi-self-test crashed in anvio 5.4.0

[xvazquezc]

Hi, Following the thread in Slack, my anvi-self-test crashed but for a different reason. Anvi'o seems to work fine though, at least with the pangenomics pipeline.

(anvi-54) $ anvi-self-test 

:: Output directory ...

/tmp/tmpu0lcsyp8/test-output

:: Anvo'o version ...

Anvi'o version ...............................: margaret (v5.4)
Profile DB version ...........................: 31
Contigs DB version ...........................: 12
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1

:: Initializing raw BAM files ...

Sorted BAM File ..............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-01.bam                                                                                          
BAM File Index ...............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-01.bam.bai                                                                                      

Sorted BAM File ..............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-02.bam                                                                                          
BAM File Index ...............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-02.bam.bai                                                                                      

Sorted BAM File ..............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-03.bam                                                                                          
BAM File Index ...............................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-03.bam.bai                                                                                      

:: Reformat the contigs FASTA ...

Input ........................................: sandbox/contigs.fa
Output .......................................: /tmp/tmpu0lcsyp8/test-output/contigs.fa
Minimum length ...............................: 0
Total num contigs ............................: 6
Total num nucleotides ........................: 57,030
Contigs removed ..............................: 0 (0.00% of all)
Nucleotides removed ..........................: 0 (0.00% of all)
Deflines simplified ..........................: True

test_prefix_000000000001  204_10M_MERGED.PERFECT.gz.keep_contig_878
test_prefix_000000000002  204_10M_MERGED.PERFECT.gz.keep_contig_6515
test_prefix_000000000003  204_10M_MERGED.PERFECT.gz.keep_contig_1720
test_prefix_000000000004  contig_1
test_prefix_000000000005  contig_2
test_prefix_000000000006  contig_3

:: Generating a new contigs database with external gene calls ...

Input FASTA file .............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB with external gene calls
Description ..................................: No description is given
Split Length .................................: 1,000                                                                                                                               
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: sandbox/example_external_gene_calls.txt
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True
External gene calls ..........................: 49 gene calls recovered and will be processed.

WARNING
===============================================
6 of your 49 gene calls were impartial, hence the translated amino acid
sequences for those were not stored in the database.

Contigs with at least one gene call ..........: 6 of 6 (100.0%)                                                                                                                     
Contigs database .............................: A new database, /tmp/tmpu0lcsyp8/test-output/CONTIGS.db, has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (wnat anvi'o gave back) .: 1,620

:: Generating a new contigs database with the default gene caller ...

Input FASTA file .............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/tests/sandbox/contigs.fa
Name .........................................: Contigs DB for anvi'o self-tests
Description ..................................: No description is given
Split Length .................................: 1,000                                                                                                                               
K-mer size ...................................: 4
Skip gene calling? ...........................: False
External gene calls provided? ................: None
Ignoring internal stop codons? ...............: False
Splitting pays attention to gene calls? ......: True

Finding ORFs in contigs
===============================================
Genes ........................................: /tmp/tmpzkhbi1a4/contigs.genes
Amino acid sequences .........................: /tmp/tmpzkhbi1a4/contigs.amino_acid_sequences
Log file .....................................: /tmp/tmpzkhbi1a4/00_log.txt
Result .......................................: Prodigal (v2.6.3) has identified 51 genes.                                                                                          

Contigs with at least one gene call ..........: 6 of 6 (100.0%)                                                                                                                     
Contigs database .............................: A new database, /tmp/tmpu0lcsyp8/test-output/CONTIGS.db, has been created.
Number of contigs ............................: 6
Number of splits .............................: 38
Total number of nucleotides ..................: 57,030
Gene calling step skipped ....................: False
Splits broke genes (non-mindful mode) ........: False
Desired split length (what the user wanted) ..: 1,000
Average split length (wnat anvi'o gave back) .: 1,620

:: Displaying the info for the contigs databse ...

DB Info (no touch)
===============================================
Database Path ................................: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 12

DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o self-tests
contigs_db_hash ..............................: hash06ae7042
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
splits_consider_gene_calls ...................: 1
creation_date ................................: 1552257404.8492

* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be very
skeptical. For instance, if the programmer asks you to change the values for
'num_contigs', or 'kmer_size', it would mean that they likely hate you and want
you to fail. So please be extremely careful changing any of these values.

:: Setting a new self value in the self table of the contigs databse ...

WARNING
===============================================
You are about to set a new key, 'a_new_test_key', in the self table of your
contigs database which will hold the value 'a new test value'.

DB Info (no touch)
===============================================
Database Path ................................: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db
Description ..................................: [Not found, but it's OK]
Type .........................................: contigs
Version ......................................: 12

DB Info (no touch also)
===============================================
project_name .................................: Contigs DB for anvi'o self-tests
contigs_db_hash ..............................: hash06ae7042
split_length .................................: 1000
kmer_size ....................................: 4
num_contigs ..................................: 6
total_length .................................: 57030
num_splits ...................................: 38
gene_level_taxonomy_source ...................: None
gene_function_sources ........................: None
genes_are_called .............................: 1
splits_consider_gene_calls ...................: 1
creation_date ................................: 1552257404.8492
a_new_test_key [JUST SET] ....................: a new test value

* Please remember that it is never a good idea to change these values. But in some
cases it may be absolutely necessary to update something here, and a programmer
may ask you to run this program and do it. But even then, you should be very
skeptical. For instance, if the programmer asks you to change the values for
'num_contigs', or 'kmer_size', it would mean that they likely hate you and want
you to fail. So please be extremely careful changing any of these values.

:: Exporting gene calls from the contigs database ...

Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        
Num gene calls found .........................: 51
Output .......................................: /tmp/tmpu0lcsyp8/test-output/exported_gene_calls.txt

:: Exporting contig sequences from the contigs database ...

Export mode ..................................: contigs
Output FASTA .................................: /tmp/tmpu0lcsyp8/test-output/exported_contig_seqeunces.fa

:: Exporting contig sequences from the contigs database in 'splits mode' ...

Export mode ..................................: splits
Output FASTA .................................: /tmp/tmpu0lcsyp8/test-output/exported_split_seqeunces.fa

:: Populating taxonomy for splits table in the database using 'centrifuge' parser ...

Total num hits found .........................: 49
Removed due to low hit score of 250 ..........: 17
Removed due to too many competing hits .......: 0
Final num hits ...............................: 23
Num gene caller ids in the db ................: 51                                                                                                                                  
Num gene caller ids in the incoming data .....: 23
Taxon names table ............................: Updated with 1 unique taxon names
Genes taxonomy table .........................: Taxonomy stored for 23 gene calls
Splits taxonomy ..............................: Input data from "centrifuge" annotated 17 of 38 splits (44.7%) with taxonomy.

:: Trying to remove HMM sources from the contigs database (when there are none in it) ...

WARNING
===============================================
The HMM tables in your contigs databse is empty. Now anvi'o will quit and go
back to sleep.

:: Populating HMM hits tables in the latest contigs database using default HMM profiles ...

Target found .................................: AA:GENE                                                                                                                             
Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        

WARNING
===============================================
You did not provide any gene caller ids. As a result, anvi'o will give you back
sequences for every 51 gene call stored in the contigs database.

Output .......................................: /tmp/tmpj6468vfa/AA_gene_sequences.fa                                                                                               
Target found .................................: RNA:CONTIG
Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        

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 ...............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/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 .......: 2
Temporary work dir ...........................: /tmp/tmpk7w_0hlr
HMM scan output ..............................: /tmp/tmpk7w_0hlr/hmm.output
HMM scan hits ................................: /tmp/tmpk7w_0hlr/hmm.hits
Log file .....................................: /tmp/tmpk7w_0hlr/00_log.txt
Number of raw hits ...........................: 0                                                                                                                                   

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

HMM Profiling for Campbell_et_al
===============================================
Reference ....................................: Campbell et al, http://www.pnas.org/content/110/14/5540.short
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: bacteria
HMM model path ...............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/data/hmm/Campbell_et_al/genes.hmm.gz
Number of genes ..............................: 139
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 2
Temporary work dir ...........................: /tmp/tmpf3v1bidd
HMM scan output ..............................: /tmp/tmpf3v1bidd/hmm.output
HMM scan hits ................................: /tmp/tmpf3v1bidd/hmm.hits
Log file .....................................: /tmp/tmpf3v1bidd/00_log.txt
Number of raw hits ...........................: 2                                                                                                                                   

HMM Profiling for BUSCO_83_Protista
===============================================
Reference ....................................: See Simao et al, doi:10.1093/bioinformatics/btv351, as well as http://merenlab.org/delmont-euk-scgs
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: eukarya
HMM model path ...............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/data/hmm/BUSCO_83_Protista/genes.hmm.gz
Number of genes ..............................: 83
Noise cutoff term(s) .........................: -E 1e-25
Number of CPUs will be used for search .......: 2
Temporary work dir ...........................: /tmp/tmpxv_fm1q_
HMM scan output ..............................: /tmp/tmpxv_fm1q_/hmm.output
HMM scan hits ................................: /tmp/tmpxv_fm1q_/hmm.hits
Log file .....................................: /tmp/tmpxv_fm1q_/00_log.txt
Number of raw hits ...........................: 0                                                                                                                                   

* The HMM source 'BUSCO_83_Protista' returned 0 hits. SAD (but it's stil OK).

HMM Profiling for Rinke_et_al
===============================================
Reference ....................................: Rinke et al, http://www.nature.com/nature/journal/v499/n7459/full/nature12352.html
Kind .........................................: singlecopy
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: archaea
HMM model path ...............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/data/hmm/Rinke_et_al/genes.hmm.gz
Number of genes ..............................: 162
Noise cutoff term(s) .........................: --cut_ga
Number of CPUs will be used for search .......: 2
Temporary work dir ...........................: /tmp/tmp944_ihwe
HMM scan output ..............................: /tmp/tmp944_ihwe/hmm.output
HMM scan hits ................................: /tmp/tmp944_ihwe/hmm.hits
Log file .....................................: /tmp/tmp944_ihwe/00_log.txt
Number of raw hits ...........................: 1                                                                                                                                   

:: Populating HMM hits tables in the latest contigs database using a mock HMM collection from an external directory ...

HMM profiles .................................: 1 source been loaded: external_hmm_profile (2 genes)
Target found .................................: AA:GENE                                                                                                                             
Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        

WARNING
===============================================
You did not provide any gene caller ids. As a result, anvi'o will give you back
sequences for every 51 gene call stored in the contigs database.

Output .......................................: /tmp/tmpplln3o4q/AA_gene_sequences.fa                                                                                               

HMM Profiling for external_hmm_profile
===============================================
Reference ....................................: Anvio et al, http://merenlab.org/projects/anvio
Kind .........................................: external_hmm_genes
Alphabet .....................................: AA
Context ......................................: GENE
Domain .......................................: N\A
HMM model path ...............................: sandbox/external_hmm_profile/genes.hmm.gz
Number of genes ..............................: 2
Noise cutoff term(s) .........................: -E 1e-12
Number of CPUs will be used for search .......: 1
Temporary work dir ...........................: /tmp/tmpi8ha807d
HMM scan output ..............................: /tmp/tmpi8ha807d/hmm.output
HMM scan hits ................................: /tmp/tmpi8ha807d/hmm.hits
Log file .....................................: /tmp/tmpi8ha807d/00_log.txt
Number of raw hits ...........................: 4                                                                                                                                   

:: Rerunning HMMs for a specific installed profile ...

Target found .................................: RNA:CONTIG                                                                                                                          
Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        

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 ...............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/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 ...........................: /tmp/tmpijvc7_jl
HMM scan output ..............................: /tmp/tmpijvc7_jl/hmm.output
HMM scan hits ................................: /tmp/tmpijvc7_jl/hmm.hits
Log file .....................................: /tmp/tmpijvc7_jl/00_log.txt
Number of raw hits ...........................: 0                                                                                                                                   

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

WARNING
===============================================
Previous entries for "Ribosomal_RNAs" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits"

:: Listing all available HMM sources in the contigs database ...

* Campbell_et_al [type: singlecopy] [num genes: 139]                                                                                                                                
* BUSCO_83_Protista [type: singlecopy] [num genes: 83]
* Rinke_et_al [type: singlecopy] [num genes: 162]
* external_hmm_profile [type: external_hmm_genes] [num genes: 2]
* Ribosomal_RNAs [type: Ribosomal_RNAs] [num genes: 12]

:: Removing HMM hits for Rinke_et_al from the contigs database ...

WARNING
===============================================
Previous entries for "Rinke_et_al" is being removed from "hmm_hits_info,
hmm_hits, hmm_hits_in_splits"

:: Export genomic locus using HMM ...

Input / Output
===============================================
Contigs DB ...................................: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db
Output directory .............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/tests
Genes to report ..............................: 22 genes before the matching gene, and 22 that follow
Rev-comp the locus sequence if necessary .....: True

Initialization bleep bloops
===============================================
Mode .........................................: HMM search
Search term ..................................: S-AdoMet_synt_C                                                                                                                     
HMM sources being used .......................: Campbell_et_al
Matching genes ...............................: 1 genes matched your search

Exporting locus 1 of 1
===============================================
Contig name ..................................: 204_10M_MERGED.PERFECT.gz.keep_contig_878
Contig length ................................: 27,538
Num genes in contig ..........................: 23
Target gene call .............................: 9
Target gene direction ........................: Forward
First and last gene of the locus (raw) .......: -13 and 31

* A premature locus is found .. the current configuration says 'whatevs'. Anvi'o
will continue.

First and last gene of the locus (final) .....: 0 and 22
Locus gene call start/stops excess (nts) .....: 0
Reverse complementing everything .............: False
Output FASTA file ............................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001.fa
Output contigs DB path .......................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001.db                                                                        
Output blank profile DB path .................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001-PROFILE/PROFILE.db

:: Recovering completeness esimates for the contigs db ...

Completeness for 38 splits (p < 1e-15)
===============================================
Campbell_et_al (bacterial SCGs) ..............: 1.44% complete, 0.00% redundant
BUSCO_83_Protista (eukaryal SCGs) ............: 0.00% complete, 0.00% redundant

:: Importing gene function calls using 'interproscan' parser ...

Gene functions ...............................: 273 function calls from 11 sources for 48 unique gene calls has been added to the contigs database.

:: Importing gene function calls INCREMENTALLY using a TAB-delimited default input matrix ...

WARNING
===============================================
Some of the annotation sources you want to add into the database are already in
the db. So anvi'o will REPLACE those with the incoming data from these sources:
Pfam, TIGRFAM

Gene functions ...............................: 88 function calls from 2 sources for 41 unique gene calls has been added to the contigs database.

:: REPLACING gene function calls using a TAB-delimited default input matrix ...

WARNING
===============================================
As per your request, anvi'o is DROPPING all previous function calls from 11
sources before adding the incoming data, which contains 88 entries originating
from 2 sources: Pfam, TIGRFAM

Gene functions ...............................: 88 function calls from 2 sources for 41 unique gene calls has been added to the contigs database.

:: Listing all available function call sources in the contigs database ...

ANNOTATION SOURCES FOUND
===============================================
* Pfam
* TIGRFAM

:: Export all functional annotations ...

Annotation sources ...........................: Pfam, TIGRFAM.                                                                                                                      
Number of annotations reported ...............: 88                                                                                                                                  
Output file ..................................: /tmp/tmpu0lcsyp8/test-output/exported_functions_from_all_sources.txt

gene_callers_id  source   accession  function                                                    e_value
1                Pfam     PF01132    Elongation factor P (EF-P) OB domain                        4e-23
1                Pfam     PF08207    Elongation factor P (EF-P) KOW-like domain                  3e-25
1                Pfam     PF09285    Elongation factor P, C-terminal                             3.1e-24
1                TIGRFAM  TIGR00038  efp: translation elongation factor P                        1.5e-75
2                Pfam     PF01029    NusB family                                                 2.5e-30
2                TIGRFAM  TIGR01951  nusB: transcription antitermination factor NusB             1.5e-36
3                Pfam     PF00117    Glutamine amidotransferase class-I                          2e-36
3                Pfam     PF00988    Carbamoyl-phosphate synthase small chain, CPSase domain     1.2e-48
3                TIGRFAM  TIGR01368  CPSaseIIsmall: carbamoyl-phosphate synthase, small subunit  1.5e-132

:: Export genomic locus using functional annotation search ...

Input / Output
===============================================
Contigs DB ...................................: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db
Output directory .............................: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/tests
Genes to report ..............................: 22 genes before the matching gene, and 22 that follow
Rev-comp the locus sequence if necessary .....: True

Initialization bleep bloops
===============================================
Mode .........................................: Function search
Search term ..................................: NusB                                                                                                                                
Function calls being used ....................: TIGRFAM, Pfam
Matching genes ...............................: 1 genes matched your search                                                                                                         

Exporting locus 1 of 1
===============================================
Contig name ..................................: 204_10M_MERGED.PERFECT.gz.keep_contig_878
Contig length ................................: 27,538
Num genes in contig ..........................: 23
Target gene call .............................: 2
Target gene direction ........................: Forward
First and last gene of the locus (raw) .......: -20 and 24

* A premature locus is found .. the current configuration says 'whatevs'. Anvi'o
will continue.

First and last gene of the locus (final) .....: 0 and 22
Locus gene call start/stops excess (nts) .....: 0
Reverse complementing everything .............: False
Output FASTA file ............................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_functions_0001.fa
Output contigs DB path .......................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_functions_0001.db                                                                  
Output blank profile DB path .................: /tmp/tmpu0lcsyp8/test-output/exported_locus_from_functions_0001-PROFILE/PROFILE.db

:: Export only Pfam annotations ...

Annotation sources ...........................: Pfam, TIGRFAM.                                                                                                                      
Requested sources ............................: Pfam.
Number of annotations reported ...............: 61                                                                                                                                  
Output file ..................................: /tmp/tmpu0lcsyp8/test-output/exported_functions_from_source_Pfam.txt

gene_callers_id  source  accession  function                                                  e_value
1                Pfam    PF01132    Elongation factor P (EF-P) OB domain                      4e-23
1                Pfam    PF08207    Elongation factor P (EF-P) KOW-like domain                3e-25
1                Pfam    PF09285    Elongation factor P, C-terminal                           3.1e-24
2                Pfam    PF01029    NusB family                                               2.5e-30
3                Pfam    PF00117    Glutamine amidotransferase class-I                        2e-36
3                Pfam    PF00988    Carbamoyl-phosphate synthase small chain, CPSase domain   1.2e-48
4                Pfam    PF02142    MGS-like domain                                           8.8e-14
4                Pfam    PF02786    Carbamoyl-phosphate synthase L chain, ATP binding domain  5.6e-66
4                Pfam    PF02786    Carbamoyl-phosphate synthase L chain, ATP binding domain  7.9e-37

:: Contigs DB is ready; here are the tables in it: ...

collections_bins_info      hmm_hits                 
collections_info           hmm_hits_in_splits       
collections_of_contigs     hmm_hits_info            
collections_of_splits      kmer_contigs             
contig_sequences           kmer_splits              
contigs_basic_info         nt_position_info         
gene_amino_acid_sequences  self                     
gene_functions             splits_basic_info        
genes_in_contigs           splits_taxonomy          
genes_in_splits            taxon_names              
genes_taxonomy           

:: Generating a 'blank profile' with the newly generated contigs database ...

Contigs DB .........................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                                  

WARNING
=====================================
You are about to generate a blank profile. This is what we do when we have
nothing but a contigs database to play with. Because anvi'o is lazy, it will not
check the rest of the parameters you may have declred. Most of them will not
matter.

WARNING
=====================================
Amino acid linkmer frequencies will not be characterized for this profile.

anvio ..............................: 5.4
profiler_version ...................: 31
sample_id ..........................: BLANK
description ........................: None
profile_db .........................: /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/PROFILE.db
contigs_db .........................: True
contigs_db_hash ....................: hash06ae7042
cmd_line ...........................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-profile -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db -o /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE -S BLANK --blank-profile
merged .............................: False
blank ..............................: True
split_length .......................: 1,000
min_contig_length ..................: 1,000
max_contig_length ..................: 9,223,372,036,854,775,807
min_mean_coverage ..................: 0
clustering_performed ...............: True
min_coverage_for_variability .......: 10
skip_SNV_profiling .................: False
profile_SCVs .......................: False
report_variability_full ............: False

WARNING
=====================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

input_bam ..........................: None                                                                                                                                          
output_dir .........................: /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE
total_reads_mapped .................: 0
num_contigs ........................: 6
num_contigs_after_M ................: 3
num_splits .........................: 35
total_length .......................: 56,709

New data for 'layers' in data group 'default'
=====================================
Data key "total_reads_mapped" ......: Predicted type: int

NEW DATA
=====================================
Database ...........................: profile
Data group .........................: default
Data table .........................: layers
New data keys ......................: total_reads_mapped.

New items order ....................: "tnf:euclidean:ward" (type newick) has been added to the database...                                                                          
New items order ....................: "tnf-splits:euclidean:ward" (type newick) has been added to the database...                                                                   

* Happy 😇

:: Importing a collection into the blank profile ...

Item names in input ..........................: 26
Num bins in input ............................: 2

WARNING
===============================================
Since you are working with a blank proifle, anvi'o is not going to check whether
the names item names in your collections file matches to the item names in other
databases of yours. It is all fine for now, but this requires you to be even
extra careful with your downstream analyses in case stuff hits the fan later.

Items in profile database ....................: 26
Item names shared between input and db .......: 26
Collections ..................................: The collection "collection_blank" that describes 26 splits and 2 bins has been successfully added to the database at "/tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/PROFILE.db". Here is a full list of the bin names in this collection: Bin_2,Bin_1.

:: Summarizing the collection stored in the blank profile ...

Contigs DB ...................................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                        
Auxiliary Data ...............................: Found: /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/AUXILIARY-DATA.db (v. 2)                                                          
Profile Super ................................: Initialized with all 38 splits: /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/PROFILE.db (v. 31)
Splits taxonomy ..............................: Initiated for taxonomic level for "t_genus"                                                                                         

Misc data reported for layers ................: default

Misc data reported for items .................: None

HTML Output ..................................: /tmp/tmpu0lcsyp8/test-output/BLANK-SUMMARY/index.html

:: Profiling sample SAMPLE-01 ...

Contigs DB .........................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                                  
anvio ..............................: 5.4                                                                                                                                           
profiler_version ...................: 31
sample_id ..........................: SAMPLE_01
description ........................: None
profile_db .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-01/PROFILE.db
contigs_db .........................: True
contigs_db_hash ....................: hash06ae7042
cmd_line ...........................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-profile -i /tmp/tmpu0lcsyp8/test-output/SAMPLE-01.bam -o /tmp/tmpu0lcsyp8/test-output/SAMPLE-01 -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db --profile-SCVs
merged .............................: False
blank ..............................: False
split_length .......................: 1,000
min_contig_length ..................: 1,000
max_contig_length ..................: 9,223,372,036,854,775,807
min_mean_coverage ..................: 0
clustering_performed ...............: False
min_coverage_for_variability .......: 10
skip_SNV_profiling .................: False
profile_SCVs .......................: True
report_variability_full ............: False

WARNING
=====================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

input_bam ..........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-01.bam                                                                                                    
output_dir .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-01
total_reads_mapped .................: 23,783
num_contigs ........................: 3
num_contigs_after_M ................: 3
num_splits .........................: 35
total_length .......................: 56,709

New data for 'layers' in data group 'default'
=====================================
Data key "total_reads_mapped" ......: Predicted type: int
Data key "num_SNVs_reported" .......: Predicted type: int

NEW DATA
=====================================
Database ...........................: profile
Data group .........................: default
Data table .........................: layers
New data keys ......................: total_reads_mapped, num_SNVs_reported.

* Happy 😇

:: Importing short-read-level taxonomy for SAMPLE-01 ...

Total num hits found .........................: 18
Total num non-zero-count hits ................: 18
* 1 entries added into layers additional data as data group 't_domain'                                                                                                              
* 2 entries added into layers additional data as data group 't_phylum'                                                                                                              
* 2 entries added into layers additional data as data group 't_class'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.02% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_order'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.02% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_family'                                                                                                              

WARNING
===============================================
A total of 1 taxon names, which made up 0.02% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_genus'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.02% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 3 entries added into layers additional data as data group 't_species'                                                                                                             

WARNING
===============================================
A total of 2 taxon names, which made up 0.12% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

:: Profiling sample SAMPLE-02 ...

Contigs DB .........................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                                  
anvio ..............................: 5.4                                                                                                                                           
profiler_version ...................: 31
sample_id ..........................: SAMPLE_02
description ........................: None
profile_db .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-02/PROFILE.db
contigs_db .........................: True
contigs_db_hash ....................: hash06ae7042
cmd_line ...........................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-profile -i /tmp/tmpu0lcsyp8/test-output/SAMPLE-02.bam -o /tmp/tmpu0lcsyp8/test-output/SAMPLE-02 -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db --profile-SCVs
merged .............................: False
blank ..............................: False
split_length .......................: 1,000
min_contig_length ..................: 1,000
max_contig_length ..................: 9,223,372,036,854,775,807
min_mean_coverage ..................: 0
clustering_performed ...............: False
min_coverage_for_variability .......: 10
skip_SNV_profiling .................: False
profile_SCVs .......................: True
report_variability_full ............: False

WARNING
=====================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

input_bam ..........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-02.bam                                                                                                    
output_dir .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-02
total_reads_mapped .................: 5,082
num_contigs ........................: 3
num_contigs_after_M ................: 3
num_splits .........................: 35
total_length .......................: 56,709

New data for 'layers' in data group 'default'
=====================================
Data key "total_reads_mapped" ......: Predicted type: int
Data key "num_SNVs_reported" .......: Predicted type: int

NEW DATA
=====================================
Database ...........................: profile
Data group .........................: default
Data table .........................: layers
New data keys ......................: total_reads_mapped, num_SNVs_reported.

* Happy 😇

:: Importing short-read-level taxonomy for SAMPLE-02 ...

Total num hits found .........................: 13
Total num non-zero-count hits ................: 13
* 1 entries added into layers additional data as data group 't_domain'                                                                                                              
* 1 entries added into layers additional data as data group 't_phylum'                                                                                                              

WARNING
===============================================
A total of 1 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 1 entries added into layers additional data as data group 't_class'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 1 entries added into layers additional data as data group 't_order'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 1 entries added into layers additional data as data group 't_family'                                                                                                              

WARNING
===============================================
A total of 1 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 1 entries added into layers additional data as data group 't_genus'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_species'                                                                                                             

WARNING
===============================================
A total of 2 taxon names, which made up 0.17% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

:: Profiling sample SAMPLE-03 ...

Contigs DB .........................: Initialized: /tmp/tmpu0lcsyp8/test-output/CONTIGS.db (v. 12)                                                                                  
anvio ..............................: 5.4                                                                                                                                           
profiler_version ...................: 31
sample_id ..........................: SAMPLE_03
description ........................: None
profile_db .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-03/PROFILE.db
contigs_db .........................: True
contigs_db_hash ....................: hash06ae7042
cmd_line ...........................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-profile -i /tmp/tmpu0lcsyp8/test-output/SAMPLE-03.bam -o /tmp/tmpu0lcsyp8/test-output/SAMPLE-03 -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db --profile-SCVs
merged .............................: False
blank ..............................: False
split_length .......................: 1,000
min_contig_length ..................: 1,000
max_contig_length ..................: 9,223,372,036,854,775,807
min_mean_coverage ..................: 0
clustering_performed ...............: False
min_coverage_for_variability .......: 10
skip_SNV_profiling .................: False
profile_SCVs .......................: True
report_variability_full ............: False

WARNING
=====================================
Your minimum contig length is set to 1,000 base pairs. So anvi'o will not take
into consideration anything below that. If you need to kill this an restart your
analysis with another minimum contig length value, feel free to press CTRL+C.

input_bam ..........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-03.bam                                                                                                    
output_dir .........................: /tmp/tmpu0lcsyp8/test-output/SAMPLE-03
total_reads_mapped .................: 24,870
num_contigs ........................: 3
num_contigs_after_M ................: 3
num_splits .........................: 35
total_length .......................: 56,709

New data for 'layers' in data group 'default'
=====================================
Data key "total_reads_mapped" ......: Predicted type: int
Data key "num_SNVs_reported" .......: Predicted type: int

NEW DATA
=====================================
Database ...........................: profile
Data group .........................: default
Data table .........................: layers
New data keys ......................: total_reads_mapped, num_SNVs_reported.

* Happy 😇

:: Importing short-read-level taxonomy for SAMPLE-03 ...

Total num hits found .........................: 22
Total num non-zero-count hits ................: 22
* 1 entries added into layers additional data as data group 't_domain'                                                                                                              
* 2 entries added into layers additional data as data group 't_phylum'                                                                                                              
* 2 entries added into layers additional data as data group 't_class'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.04% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_order'                                                                                                               

WARNING
===============================================
A total of 1 taxon names, which made up 0.04% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_family'                                                                                                              

WARNING
===============================================
A total of 2 taxon names, which made up 0.04% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 2 entries added into layers additional data as data group 't_genus'                                                                                                               

WARNING
===============================================
A total of 2 taxon names, which made up 0.04% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

* 3 entries added into layers additional data as data group 't_species'                                                                                                             

WARNING
===============================================
A total of 4 taxon names, which made up 0.08% of the input data altogether were
excluded from this import due to the min abundance criterion of 0.1% for
inclusion.

:: Merging profiles ...

WARNING
===============================================
The CONCOCT module could not be imported :( Anvi'o will still be able to perform
the merging, however, the unsupervised binning results will not be available to
you in the resulting merged profile database. This is what the module was upset
about: '''/home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-
packages/anvio/../../../libgsl.so.23: undefined symbol: cblas_dasum''', in case
you would like to fix this problem.

WARNING
===============================================
Pleae read carefuly. You sent 6 profile databases to anvi'o merger to be merged.
However, not all of them were single, non-blank anvi'o profiles. Anvi'o removed
3 of them, and will merge only the remaining 3. At the end of this warning you
will find a list of paths to those databases anvi'o excluded from merging. If
you are not happy with that, please carefully examine what went wrong. Here are
all the paths for excluded databases: '/tmp/tmpu0lcsyp8/test-output/BLANK-
PROFILE/PROFILE.db', '/tmp/tmpu0lcsyp8/test-
output/exported_locus_from_functions_0001-PROFILE/PROFILE.db',
'/tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001-PROFILE/PROFILE.db'.

GOOD NEWS
===============================================
Anvi'o found 7 data groups for taxonomy (t_genus, t_species, t_family, t_phylum,
t_domain, t_class, t_order), and will do its best to make sure they get worked
into the merged profile database. A moment of zero promises but crossed fingers
(which is the best way to avoid most computational poopsies).

WARNING
===============================================
Anvi'o just set the normalization values for each sample based on how many
mapped reads they contained. This information will only be used to calculate the
normalized coverage table. Here are those values: SAMPLE_01: 0.21, SAMPLE_02:
1.00, SAMPLE_03: 0.20

profiler_version .............................: 31
output_dir ...................................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED
sample_id ....................................: SAMPLES_MERGED
description ..................................: Found (2230 characters)
profile_db ...................................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/PROFILE.db
merged .......................................: True
contigs_db_hash ..............................: hash06ae7042
num_runs_processed ...........................: 3
merged_sample_ids ............................: SAMPLE_01, SAMPLE_02, SAMPLE_03
Common layer additional data keys ............: default, t_genus, t_species, t_family, t_phylum, t_domain, t_class, t_order
total_reads_mapped ...........................: 23783, 5082, 24870
cmd_line .....................................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-merge /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/exported_locus_from_functions_0001-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-01/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-02/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-03/PROFILE.db -o /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db --description sandbox/example_description.md
clustering_performed .........................: True

* Anvi'o hierarchical clustering of contigs...

New items order ..............................: "tnf-cov:euclidean:ward" (type newick) has been added to the database...                                                            
New items order ..............................: "tnf:euclidean:ward" (type newick) has been added to the database...                                                                
New items order ..............................: "cov:euclidean:ward" (type newick) has been added to the database...                                                                

* Additional data and layer orders...

Auxiliary Data ...............................: Found: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/AUXILIARY-DATA.db (v. 2)                                                         
Profile Super ................................: Initialized with all 35 splits: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/PROFILE.db (v. 31)

Layer orders added
===============================================
* std_coverage
* mean_coverage
* mean_coverage_Q2Q3
* max_normalized_ratio
* relative_abundance
* detection
* abundance
* variability

Data groups added
===============================================
* default (w/2 items)
* t_genus (w/2 items)
* t_species (w/3 items)
* t_family (w/2 items)
* t_phylum (w/2 items)
* t_domain (w/1 items)
* t_class (w/2 items)
* t_order (w/2 items)

* Happy ☘

:: Merging profiles without any clustering ...

WARNING
===============================================
The CONCOCT module could not be imported :( Anvi'o will still be able to perform
the merging, however, the unsupervised binning results will not be available to
you in the resulting merged profile database. This is what the module was upset
about: '''/home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-
packages/anvio/../../../libgsl.so.23: undefined symbol: cblas_dasum''', in case
you would like to fix this problem.

WARNING
===============================================
Pleae read carefuly. You sent 7 profile databases to anvi'o merger to be merged.
However, not all of them were single, non-blank anvi'o profiles. Anvi'o removed
4 of them, and will merge only the remaining 3. At the end of this warning you
will find a list of paths to those databases anvi'o excluded from merging. If
you are not happy with that, please carefully examine what went wrong. Here are
all the paths for excluded databases: '/tmp/tmpu0lcsyp8/test-output/BLANK-
PROFILE/PROFILE.db', '/tmp/tmpu0lcsyp8/test-
output/exported_locus_from_functions_0001-PROFILE/PROFILE.db',
'/tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001-PROFILE/PROFILE.db',
'/tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/PROFILE.db'.

GOOD NEWS
===============================================
Anvi'o found 7 data groups for taxonomy (t_genus, t_species, t_phylum, t_domain,
t_class, t_order, t_family), and will do its best to make sure they get worked
into the merged profile database. A moment of zero promises but crossed fingers
(which is the best way to avoid most computational poopsies).

WARNING
===============================================
Anvi'o just set the normalization values for each sample based on how many
mapped reads they contained. This information will only be used to calculate the
normalized coverage table. Here are those values: SAMPLE_01: 0.21, SAMPLE_02:
1.00, SAMPLE_03: 0.20

profiler_version .............................: 31
output_dir ...................................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED-WO-CLUSTERING
sample_id ....................................: SAMPLES_MERGED_WO_CLUSTERING
description ..................................: None
profile_db ...................................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED-WO-CLUSTERING/PROFILE.db
merged .......................................: True
contigs_db_hash ..............................: hash06ae7042
num_runs_processed ...........................: 3
merged_sample_ids ............................: SAMPLE_01, SAMPLE_02, SAMPLE_03
Common layer additional data keys ............: default, t_genus, t_species, t_phylum, t_domain, t_class, t_order, t_family
total_reads_mapped ...........................: 23783, 5082, 24870
cmd_line .....................................: /home/xabi/anaconda2/envs/anvi-54/bin/anvi-merge /tmp/tmpu0lcsyp8/test-output/BLANK-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/exported_locus_from_functions_0001-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/exported_locus_from_hmm_0001-PROFILE/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-01/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-02/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLE-03/PROFILE.db /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/PROFILE.db -o /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED-WO-CLUSTERING -c /tmp/tmpu0lcsyp8/test-output/CONTIGS.db --skip-concoct-binning --skip-hierarchical-clustering
clustering_performed .........................: False

* Anvi'o hierarchical clustering of contigs...

* Additional data and layer orders...

Auxiliary Data ...............................: Found: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED-WO-CLUSTERING/AUXILIARY-DATA.db (v. 2)                                           
Profile Super ................................: Initialized with all 35 splits: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED-WO-CLUSTERING/PROFILE.db (v. 31)

Layer orders added
===============================================
* std_coverage
* mean_coverage
* mean_coverage_Q2Q3
* max_normalized_ratio
* relative_abundance
* detection
* abundance
* variability

Data groups added
===============================================
* default (w/2 items)
* t_genus (w/2 items)
* t_species (w/3 items)
* t_phylum (w/2 items)
* t_domain (w/1 items)
* t_class (w/2 items)
* t_order (w/2 items)
* t_family (w/2 items)

* Happy ☘

:: Update the description in the merged profile ...

* The anvi'o profile database has just been updated with a description that
contains 274 words and 2230 characters.

:: Generating coverages and sequences files for splits (for external binning) ...

Coverages file ...............................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/SAMPLES_MERGED-COVs.txt
Sequences file ...............................: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/SAMPLES_MERGED-SPLITS.fa

:: Generating per-nt position coverage values for a single split across samples ...

Auxiliary Data ...............................: Found: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/AUXILIARY-DATA.db (v. 2)                                                         
Profile Super ................................: Initialized with all 35 splits: /tmp/tmpu0lcsyp8/test-output/SAMPLES-MERGED/PROFILE.db (v. 31)
Num splits ...................................: 1
Sample names .................................: SAMPLE_01, SAMPLE_02, SAMPLE_03
Output .......................................: 7557 entries for 1 splits in 3 samples are stored in /tmp/tmpu0lcsyp8/test-output/contig_1720_split_00001_coverages.txt             

:: Generating per-nt position coverage values for splits in a bin across samples ...

WARNING
===============================================
ProfileSuperClass found a collection focus, which means it will be initialized
using only the splits in the profile database that are affiliated with the
collection CONCOCT and bins "Bin_1" it describes.

Config Error: The collection id "CONCOCT" does not seem to be in the profile database. These
              are the collections that are available through this profile database: "".     

Config Error: According to the exit code ('255'), 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.                                                                

Anvi'o version:

(anvi-54) $ anvi-self-test --version
Anvi'o version ...............................: margaret (v5.4)
Profile DB version ...........................: 31
Contigs DB version ...........................: 12
Pan DB version ...............................: 13
Genome data storage version ..................: 6
Auxiliary data storage version ...............: 2
Structure DB version .........................: 1

and my conda environment:

(anvi-54) $ conda list
# packages in environment at /home/xabi/anaconda2/envs/anvi-54:
#
# Name                    Version                   Build  Channel
anvio                     5.4.0                         0    bioconda
anvio-minimal             5.4.0            py36hf3f1cc3_0    bioconda
appdirs                   1.4.3                      py_1    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
atk                       2.25.90           hb9dd440_1002    conda-forge
attrs                     19.1.0                     py_0    conda-forge
bcftools                  1.9                  h47928c2_2    bioconda
biopython                 1.70                np112py36_1    bioconda
blas                      1.0                         mkl  
blast                     2.5.0                hc0b0e79_3    bioconda
blast-legacy              2.2.26                        1    bioconda
boost                     1.69.0          py36h8619c78_1001    conda-forge
boost-cpp                 1.69.0            h11c811c_1000    conda-forge
bottle                    0.12.13                    py_1    conda-forge
bowtie2                   2.3.4.3          py36he860b03_1    bioconda
bwa                       0.7.17               h84994c4_5    bioconda
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.16.0            ha4e643d_1000    conda-forge
centrifuge                1.0.4_beta      py36pl526he941832_2    bioconda
certifi                   2018.11.29            py36_1000    conda-forge
cffi                      1.12.2           py36h9745a5d_0    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
cherrypy                  8.0.0                    py36_0    conda-forge
colored                   1.3.93                     py_0    conda-forge
configargparse            0.13.0                     py_1    conda-forge
cryptography              2.5              py36hb7f436b_1    conda-forge
curl                      7.64.0               h646f8bb_0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
cython                    0.29.6           py36hf484d3e_0    conda-forge
datrie                    0.7.1            py36h14c3975_0    conda-forge
dbus                      1.13.0            h4e0c4b3_1000    conda-forge
diamond                   0.9.21                        1    bioconda
django                    2.0.8                    py36_0    conda-forge
docutils                  0.14                  py36_1001    conda-forge
ete3                      3.1.1                    py36_0    bioconda
expat                     2.2.5             hf484d3e_1002    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h94bbf69_1005    conda-forge
gdk-pixbuf                2.32.2                        1    bioconda
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
glib                      2.58.3            hf63aee3_1001    conda-forge
gobject-introspection     1.58.2          py36h2da5eee_1000    conda-forge
graphite2                 1.3.13            hf484d3e_1000    conda-forge
gsl                       2.4                  h14c3975_4  
gstreamer                 1.14.4            h66beb1c_1001    conda-forge
gtk2                      2.24.31           hb68c50a_1001    conda-forge
h5py                      2.9.0           nompi_py36hf008753_1102    conda-forge
harfbuzz                  2.3.1                h6824563_0    conda-forge
hdf5                      1.10.4          nompi_h11e915b_1105    conda-forge
hmmer                     3.2.1                hf484d3e_1    bioconda
htslib                    1.9                  h47928c2_5    bioconda
icu                       58.2              hf484d3e_1000    conda-forge
idna                      2.7                   py36_1002    conda-forge
illumina-utils            2.6                        py_0    bioconda
intel-openmp              2019.1                      144  
iqtree                    1.6.9                he941832_0    bioconda
jpeg                      9c                h14c3975_1001    conda-forge
jsonschema                3.0.1                    py36_0    conda-forge
kiwisolver                1.0.1           py36h6bb024c_1002    conda-forge
krb5                      1.16.3            hc83ff2d_1000    conda-forge
libcurl                   7.64.0               h01ee5af_0    conda-forge
libdeflate                1.0                  h14c3975_1    bioconda
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
libxslt                   1.1.32            h4785a14_1002    conda-forge
lxml                      4.3.2            py36h23eabaa_0    conda-forge
matplotlib                2.2.3            py36h8a2030e_1    conda-forge
matplotlib-base           2.2.3            py36h60b886d_1    conda-forge
mcl                       14.137          pl526h470a237_4    bioconda
megahit                   1.1.3                    py36_0    bioconda
mistune                   0.8.1            py36h3d5977c_0  
mkl                       2018.0.3                      1  
mmtf-python               1.1.2                      py_0    conda-forge
msgpack-python            0.6.1            py36h6bb024c_0    conda-forge
mummer                    3.23                    pl526_8    bioconda
muscle                    3.8.1551             h2d50403_3    bioconda
ncurses                   6.1               hf484d3e_1002    conda-forge
nose                      1.3.7                 py36_1002    conda-forge
numpy                     1.12.1           py36he24570b_1  
olefile                   0.46                       py_0    conda-forge
openblas                  0.3.3             h9ac9557_1001    conda-forge
openssl                   1.0.2r               h14c3975_0    conda-forge
pandas                    0.24.1           py36hf484d3e_0    conda-forge
pango                     1.40.14           h4ea9474_1004    conda-forge
patsy                     0.5.1                      py_0    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
perl                      5.26.2            h14c3975_1002    conda-forge
pillow                    5.4.1           py36h00a061d_1000    conda-forge
pip                       19.0.3                   py36_0    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
prodigal                  2.6.3                         1    bioconda
psutil                    5.4.3                    py36_0    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
pyani                     0.2.7            py36h24bf2e0_1    bioconda
pycparser                 2.19                       py_0    conda-forge
pyopenssl                 19.0.0                   py36_0    conda-forge
pyparsing                 2.3.1                      py_0    conda-forge
pyqt                      5.6.0           py36h13b7fb3_1008    conda-forge
pyrsistent                0.14.11          py36h14c3975_0    conda-forge
pysam                     0.15.2           py36h1671916_1    bioconda
pysocks                   1.6.8                 py36_1002    conda-forge
python                    3.6.7             hd21baee_1002    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python-levenshtein        0.12.0                   py36_1    bioconda
pytz                      2018.9                     py_0    conda-forge
pyyaml                    3.13            py36h14c3975_1001    conda-forge
qt                        5.6.2             hce4f676_1013    conda-forge
ratelimiter               1.2.0                 py36_1000    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
reportlab                 3.5.13          py36hbd3ef63_1000    conda-forge
requests                  2.20.0                py36_1000    conda-forge
samtools                  1.9                  h57cc563_7    bioconda
scikit-learn              0.19.2           py36h4989274_0  
scipy                     1.1.0            py36hd20e5f9_0  
seaborn                   0.9.0                      py_0    conda-forge
setuptools                40.8.0                   py36_0    conda-forge
sip                       4.18.1          py36hf484d3e_1000    conda-forge
six                       1.11.0                py36_1001    conda-forge
snakemake-minimal         5.2.4                    py36_0    bioconda
sqlite                    3.26.0            h67949de_1000    conda-forge
statsmodels               0.9.0           py36h3010b51_1000    conda-forge
tbb                       2019.4               h6bb024c_0    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
tornado                   6.0.1            py36h14c3975_0    conda-forge
trimal                    1.4.1                h2d50403_2    bioconda
urllib3                   1.23                  py36_1001    conda-forge
wheel                     0.33.1                   py36_0    conda-forge
wrapt                     1.11.1           py36h14c3975_0    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.7             h14c3975_1000    conda-forge
xorg-libxau               1.0.9                h14c3975_0    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-libxt                1.1.5             h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
yaml                      0.1.7             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

[meren]

Gawd. It seems the CONCOCT module is not running properly :/

Can you please use the files in the following directory to run anvi-cluster-with-concoct on your machine?

concoct_test.tar.gz

This is how the output messages look like in my terminal when I run the following commands in the directory above:

# show collections
$ anvi-show-collections-and-bins -p PROFILE.db

Config Error: There are no collections in this profile database. Consider making some in
              interactive mode, or importing a collection with `anvi-import-collection` (a
              tutorial on importing collections here: http://merenlab.org/2016/06/22/anvio-
              tutorial-v2/#anvi-import-collection)

# run concoct
$ anvi-cluster-with-concoct -p PROFILE.db -c CONTIGS.db
CONCOCT INIT .................................: Complete for 35 splits
CONCOCT VGBMM ................................: Requesting 400 clusters
CONCOCT VGBMM ................................: Returning 3 final clusters
Collections ..................................: The collection "CONCOCT" that describes 35 splits and 3 bins has been successfully added to the database at "PROFILE.db". Here is a full list of the bin names in this collection: Bin_2,Bin_3,Bin_1.
CONCOCT results in db ........................: PROFILE.db

# show collections again
$ anvi-show-collections-and-bins -p PROFILE.db

Collection: "CONCOCT"
===============================================
Collection ID ................................: CONCOCT
Number of bins ...............................: 3
Number of splits described ...................: 35
Bin names ....................................: Bin_1, Bin_2, Bin_3

# delete the new collection
$ anvi-delete-collection -p PROFILE.db -C CONCOCT

WARNING
===============================================
Previous entries for "CONCOCT" is being removed from "collections_info,
collections_of_contigs, collections_of_splits, collections_bins_info"

Collection delete ............................: Done. The collection "CONCOCT" is no more.

Thank you!

[xvazquezc]

Yep, CONCOCT module not working...

(anvi-54) concoct_test$ anvi-show-collections-and-bins -p PROFILE.db
[11 Mar 19 11:16:14 Accessing to the collections table] ...                                                                                                                                             

Config Error: There are no collections in this profile database. Consider making some in   
              interactive mode, or importing a collection with `anvi-import-collection` (a 
              tutorial on importing collections here: http://merenlab.org/2016/06/22/anvio-
              tutorial-v2/#anvi-import-collection)                                         

(anvi-54) concoct_test$ anvi-cluster-with-concoct -p PROFILE.db -c CONTIGS.db
Traceback (most recent call last):
  File "/home/xabi/anaconda2/envs/anvi-54/bin/anvi-cluster-with-concoct", line 9, in <module>
    import anvio.concoct as concoct
  File "/home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/concoct.py", line 33, in <module>
    import anvio.vbgmm as vbgmm
ImportError: /home/xabi/anaconda2/envs/anvi-54/lib/python3.6/site-packages/anvio/../../../libgsl.so.23: undefined symbol: cblas_dasum

[meren]

Ah. This BLAS issue again. @ozcan had recently suggested someone to rebuild their contact environment for anvi'o with an additional directive for BLAS. I think it will fix this one but I don't remember where I saw that.

[ozcan]

Hi @xvazquezc, This issue is related with openblas distribution conda installs. If you install using create -n anvio54 -c conda-forge -c bioconda anvio==5.4.0 "blas=*=openblas" it should work.

[xvazquezc]

Thanks @ozcan, that solved the CONCOCT issue. However, anvi-self-test ends with this message, but I don't see anything obvious aside of the usual warning messages:

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.                                                               

[Bio-finder]

Good morning, Is this issue fixed? We got the same issue in our lab so we just wanted to be sure that everything is working with this fix.

[meren]

Hi @Bio-finder, if you installed anvi'o through conda, @ozcan's recipe here should address it:

https://github.com/merenlab/anvio/issues/1121#issuecomment-471675728

Best,