[2023-06-30 13:24:11,477] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:11,480] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:11,480] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference
[2023-06-30 13:24:14,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:14,684] [INFO] Task started: Prodigal
[2023-06-30 13:24:14,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d39b4d7-34d7-437c-abd9-75ef59f9b077/GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz | prodigal -d GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/cds.fna -a GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:20,438] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:20,438] [INFO] Task started: HMMsearch
[2023-06-30 13:24:20,438] [INFO] Running command: hmmsearch --tblout GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/reference_markers.hmm GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:20,658] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:20,659] [INFO] Found 6/6 markers.
[2023-06-30 13:24:20,685] [INFO] Query marker FASTA was written to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta
[2023-06-30 13:24:20,686] [INFO] Task started: Blastn
[2023-06-30 13:24:20,686] [INFO] Running command: blastn -query GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/reference_markers.fasta -out GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:21,341] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:21,347] [INFO] Selected 15 target genomes.
[2023-06-30 13:24:21,347] [INFO] Target genome list was writen to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt
[2023-06-30 13:24:21,349] [INFO] Task started: fastANI
[2023-06-30 13:24:21,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d39b4d7-34d7-437c-abd9-75ef59f9b077/GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt --output GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:24:28,910] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:28,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:24:28,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:24:28,925] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 13:24:28,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 13:24:28,926] [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
Bombella favorum	strain=TMW 2.1880	GCA_014048475.1	2039164	2039164	type	True	98.9569	638	660	95	conclusive
Bombella intestini	strain=R-52487	GCA_002003665.1	1539051	1539051	type	True	94.1933	631	660	95	below_threshold
Bombella apis	strain=MRM1	GCA_014878255.1	1785988	1785988	type	True	83.3373	530	660	95	below_threshold
Bombella apis	strain=MRM1	GCA_018221685.1	1785988	1785988	type	True	83.3068	527	660	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	77.5534	75	660	95	below_threshold
Gluconobacter potus	strain=LMG 1764	GCA_001580675.1	2724927	2724927	type	True	77.5501	69	660	95	below_threshold
Acetobacter papayae	strain=JCM 25143	GCA_000613285.1	1076592	1076592	type	True	76.5619	51	660	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	76.45	58	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:24:28,928] [INFO] DFAST Taxonomy check result was written to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/tc_result.tsv
[2023-06-30 13:24:28,929] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:24:28,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:24:28,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/checkm_data
[2023-06-30 13:24:28,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:24:28,958] [INFO] Task started: CheckM
[2023-06-30 13:24:28,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/checkm_input GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/checkm_result
[2023-06-30 13:24:52,617] [INFO] Task succeeded: CheckM
[2023-06-30 13:24:52,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:24:52,640] [INFO] ===== Completeness check finished =====
[2023-06-30 13:24:52,641] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:24:52,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta)
[2023-06-30 13:24:52,642] [INFO] Task started: Blastn
[2023-06-30 13:24:52,642] [INFO] Running command: blastn -query GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd5d6ea2-3354-450a-b452-676ad63510cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:53,572] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:53,577] [INFO] Selected 8 target genomes.
[2023-06-30 13:24:53,577] [INFO] Target genome list was writen to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:24:53,615] [INFO] Task started: fastANI
[2023-06-30 13:24:53,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d39b4d7-34d7-437c-abd9-75ef59f9b077/GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:24:57,796] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:57,807] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:24:57,808] [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_014048475.1	s__Bombella favorum	98.9569	638	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002003665.1	s__Bombella intestini	94.1933	631	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221685.1	s__Bombella apis	83.3068	527	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.16	98.65	0.96	0.94	13	-
GCF_014048465.1	s__Bombella mellum	82.5681	474	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725755.1	s__Bombella sp009725755	78.5373	255	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	99.22	99.22	0.99	0.99	2	-
GCF_002592045.1	s__Bombella apium_A	78.4343	259	660	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Bombella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:24:57,810] [INFO] GTDB search result was written to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 13:24:57,810] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:24:57,814] [INFO] DFAST_QC result json was written to GCA_946477145.1_SRR10914160_bin.2_metawrap_v1.3.0_MAG_genomic.fna/dqc_result.json
[2023-06-30 13:24:57,814] [INFO] DFAST_QC completed!
[2023-06-30 13:24:57,814] [INFO] Total running time: 0h0m46s