[2024-01-24 12:30:05,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:05,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:05,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference
[2024-01-24 12:30:07,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:07,247] [INFO] Task started: Prodigal
[2024-01-24 12:30:07,247] [INFO] Running command: gunzip -c /var/lib/cwl/stga7c5e9b9-4b6b-40ae-bcd2-0cd313f3621a/GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:17,469] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:17,469] [INFO] Task started: HMMsearch
[2024-01-24 12:30:17,469] [INFO] Running command: hmmsearch --tblout GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/reference_markers.hmm GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:17,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:17,777] [INFO] Found 6/6 markers.
[2024-01-24 12:30:17,808] [INFO] Query marker FASTA was written to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-24 12:30:17,809] [INFO] Task started: Blastn
[2024-01-24 12:30:17,809] [INFO] Running command: blastn -query GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/reference_markers.fasta -out GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:18,625] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:18,630] [INFO] Selected 15 target genomes.
[2024-01-24 12:30:18,630] [INFO] Target genome list was writen to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-24 12:30:18,659] [INFO] Task started: fastANI
[2024-01-24 12:30:18,659] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c5e9b9-4b6b-40ae-bcd2-0cd313f3621a/GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:29,341] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:29,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:29,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:29,350] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:29,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:29,350] [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
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	100.0	1217	1221	95	conclusive
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	87.9368	892	1221	95	below_threshold
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	79.6445	549	1221	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	79.5866	482	1221	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	79.3838	196	1221	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	79.3069	204	1221	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	79.2182	490	1221	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.5281	420	1221	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.4096	441	1221	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	78.3075	249	1221	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.7303	347	1221	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.1177	56	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:29,358] [INFO] DFAST Taxonomy check result was written to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-24 12:30:29,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:29,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:29,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/checkm_data
[2024-01-24 12:30:29,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:29,404] [INFO] Task started: CheckM
[2024-01-24 12:30:29,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-24 12:31:01,569] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:01,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:01,583] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:01,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:01,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-24 12:31:01,584] [INFO] Task started: Blastn
[2024-01-24 12:31:01,584] [INFO] Running command: blastn -query GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stg63845bd8-070f-446a-a3dd-55e415643182/dqc_reference/reference_markers_gtdb.fasta -out GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:02,922] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:02,925] [INFO] Selected 9 target genomes.
[2024-01-24 12:31:02,925] [INFO] Target genome list was writen to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:02,934] [INFO] Task started: fastANI
[2024-01-24 12:31:02,935] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c5e9b9-4b6b-40ae-bcd2-0cd313f3621a/GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:10,271] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:10,278] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:10,278] [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_000682755.1	s__Hyphomonas beringensis	100.0	1217	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018222605.1	s__Hyphomonas sp002695785	89.368	987	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682675.1	s__Hyphomonas pacifica	87.9368	892	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCA_017792385.1	s__Hyphomonas sp017792385	80.702	621	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414505.1	s__Hyphomonas sp002414505	80.5657	529	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	-
GCF_000682715.1	s__Hyphomonas atlantica	79.6456	548	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCF_000685215.1	s__Hyphomonas jannaschiana	79.2088	491	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763715.1	s__Hyphomonas sp014763715	79.0795	481	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	78.5183	421	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:10,281] [INFO] GTDB search result was written to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:10,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:10,285] [INFO] DFAST_QC result json was written to GCF_000682755.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-24 12:31:10,285] [INFO] DFAST_QC completed!
[2024-01-24 12:31:10,285] [INFO] Total running time: 0h1m5s