[2024-01-24 13:49:29,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:29,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:29,040] [INFO] DQC Reference Directory: /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference
[2024-01-24 13:49:30,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:30,344] [INFO] Task started: Prodigal
[2024-01-24 13:49:30,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg03442029-9d8d-4d5f-b9ce-9ac3915eba10/GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/cds.fna -a GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:43,001] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:43,001] [INFO] Task started: HMMsearch
[2024-01-24 13:49:43,002] [INFO] Running command: hmmsearch --tblout GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/reference_markers.hmm GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:43,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:43,363] [INFO] Found 6/6 markers.
[2024-01-24 13:49:43,400] [INFO] Query marker FASTA was written to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:49:43,401] [INFO] Task started: Blastn
[2024-01-24 13:49:43,401] [INFO] Running command: blastn -query GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/reference_markers.fasta -out GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:44,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:44,314] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:44,315] [INFO] Target genome list was writen to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:49:44,322] [INFO] Task started: fastANI
[2024-01-24 13:49:44,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg03442029-9d8d-4d5f-b9ce-9ac3915eba10/GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna.gz --refList GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:57,300] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:57,301] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:57,315] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:57,315] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:57,316] [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
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	100.0	1336	1337	95	conclusive
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	81.0638	794	1337	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.7179	536	1337	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.2636	385	1337	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	79.0578	433	1337	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	78.6769	295	1337	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.6253	407	1337	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.5961	398	1337	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	78.5873	349	1337	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	78.5742	349	1337	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.5362	334	1337	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.5125	323	1337	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	78.51	353	1337	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.3545	358	1337	95	below_threshold
Marinobacter litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	78.3347	250	1337	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	75.4547	51	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:57,317] [INFO] DFAST Taxonomy check result was written to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:49:57,318] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:57,318] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:57,318] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/checkm_data
[2024-01-24 13:49:57,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:57,362] [INFO] Task started: CheckM
[2024-01-24 13:49:57,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/checkm_input GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:50:37,858] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:37,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,882] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:37,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:37,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:50:37,883] [INFO] Task started: Blastn
[2024-01-24 13:50:37,883] [INFO] Running command: blastn -query GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07b7a3d-b960-4edd-85e4-6828d31b2e8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:39,226] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:39,230] [INFO] Selected 18 target genomes.
[2024-01-24 13:50:39,230] [INFO] Target genome list was writen to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:39,241] [INFO] Task started: fastANI
[2024-01-24 13:50:39,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg03442029-9d8d-4d5f-b9ce-9ac3915eba10/GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna.gz --refList GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:52,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:52,689] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:52,690] [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_900114775.1	s__Marinobacter zhejiangensis	100.0	1336	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900106945.1	s__Marinobacter mobilis	81.0638	794	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.2442	386	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_002744715.1	s__Marinobacter profundi	79.0578	433	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_003315345.1	s__Marinobacter pelagius_A	78.9344	383	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994855.1	s__Marinobacter sp003994855	78.8641	399	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	78.6797	401	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	78.6659	383	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003007675.1	s__Marinobacter fuscus	78.6622	294	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	78.6344	364	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900114925.1	s__Marinobacter pelagius	78.6215	407	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	78.5473	383	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_000708045.1	s__Marinobacter nitratireducens	78.542	353	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
GCF_016820575.1	s__Marinobacter sediminum	78.5216	352	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	78.4327	350	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	78.3936	410	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_003336705.1	s__Marinobacter litoralis	78.3089	253	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.25	98.25	0.91	0.91	2	-
GCF_017301335.1	s__Marinobacter sp017301335	78.2778	344	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,691] [INFO] GTDB search result was written to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:52,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:52,699] [INFO] DFAST_QC result json was written to GCF_900114775.1_IMG-taxon_2617270916_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:50:52,699] [INFO] DFAST_QC completed!
[2024-01-24 13:50:52,699] [INFO] Total running time: 0h1m24s