[2023-06-30 20:08:44,128] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:08:44,130] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:08:44,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference
[2023-06-30 20:08:45,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:08:45,324] [INFO] Task started: Prodigal
[2023-06-30 20:08:45,324] [INFO] Running command: gunzip -c /var/lib/cwl/stgce48af1d-8c8c-439c-8740-0b441608fc07/GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna.gz | prodigal -d GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/cds.fna -a GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:08:49,511] [INFO] Task succeeded: Prodigal
[2023-06-30 20:08:49,511] [INFO] Task started: HMMsearch
[2023-06-30 20:08:49,511] [INFO] Running command: hmmsearch --tblout GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/reference_markers.hmm GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:08:49,697] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:08:49,698] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgce48af1d-8c8c-439c-8740-0b441608fc07/GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna.gz]
[2023-06-30 20:08:49,722] [INFO] Query marker FASTA was written to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta
[2023-06-30 20:08:49,722] [INFO] Task started: Blastn
[2023-06-30 20:08:49,722] [INFO] Running command: blastn -query GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/reference_markers.fasta -out GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:08:50,316] [INFO] Task succeeded: Blastn
[2023-06-30 20:08:50,320] [INFO] Selected 15 target genomes.
[2023-06-30 20:08:50,320] [INFO] Target genome list was writen to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt
[2023-06-30 20:08:50,321] [INFO] Task started: fastANI
[2023-06-30 20:08:50,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgce48af1d-8c8c-439c-8740-0b441608fc07/GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt --output GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:08:58,338] [INFO] Task succeeded: fastANI
[2023-06-30 20:08:58,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:08:58,339] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:08:58,347] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:08:58,347] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:08:58,347] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	84.9252	498	778	95	below_threshold
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	81.1885	445	778	95	below_threshold
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	81.165	436	778	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	78.8784	298	778	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	78.6572	287	778	95	below_threshold
Orbus hercynius	strain=DSM 22228	GCA_003634275.1	593135	593135	type	True	76.8335	99	778	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	76.7879	138	778	95	below_threshold
Zophobihabitans entericus	strain=IPMB12	GCA_011745665.1	1635327	1635327	type	True	76.6091	69	778	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:08:58,349] [INFO] DFAST Taxonomy check result was written to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/tc_result.tsv
[2023-06-30 20:08:58,350] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:08:58,350] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:08:58,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/checkm_data
[2023-06-30 20:08:58,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:08:58,377] [INFO] Task started: CheckM
[2023-06-30 20:08:58,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/checkm_input GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/checkm_result
[2023-06-30 20:09:17,096] [INFO] Task succeeded: CheckM
[2023-06-30 20:09:17,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:09:17,115] [INFO] ===== Completeness check finished =====
[2023-06-30 20:09:17,115] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:09:17,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta)
[2023-06-30 20:09:17,115] [INFO] Task started: Blastn
[2023-06-30 20:09:17,116] [INFO] Running command: blastn -query GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg692fdacf-a351-460b-9c11-72dbe7301883/dqc_reference/reference_markers_gtdb.fasta -out GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:09:17,997] [INFO] Task succeeded: Blastn
[2023-06-30 20:09:18,001] [INFO] Selected 6 target genomes.
[2023-06-30 20:09:18,001] [INFO] Target genome list was writen to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:09:18,002] [INFO] Task started: fastANI
[2023-06-30 20:09:18,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgce48af1d-8c8c-439c-8740-0b441608fc07/GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:09:21,283] [INFO] Task succeeded: fastANI
[2023-06-30 20:09:21,289] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:09:21,289] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003202915.1	s__Gilliamella apicola_Q	95.4726	694	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.60	95.60	0.89	0.89	2	conclusive
GCF_002142215.1	s__Gilliamella sp002142215	87.299	563	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.95	96.09	0.93	0.88	3	-
GCF_002142155.1	s__Gilliamella apis	84.9512	496	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.52	97.64	0.94	0.89	26	-
GCF_001693745.1	s__Gilliamella apicola_E	84.5178	527	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
GCF_003202775.1	s__Gilliamella apis_A	84.1254	535	778	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.23	95.38	0.94	0.89	9	-
--------------------------------------------------------------------------------
[2023-06-30 20:09:21,349] [INFO] GTDB search result was written to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 20:09:21,350] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:09:21,353] [INFO] DFAST_QC result json was written to GCA_946477435.1_SRR7287205_bin.1_metawrap_v1.3.0_MAG_genomic.fna/dqc_result.json
[2023-06-30 20:09:21,353] [INFO] DFAST_QC completed!
[2023-06-30 20:09:21,353] [INFO] Total running time: 0h0m37s