[2024-01-24 13:40:27,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:27,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:27,829] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference
[2024-01-24 13:40:29,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,158] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,158] [INFO] Running command: gunzip -c /var/lib/cwl/stg42af6834-55e1-49a2-8b1d-3a151c1d0275/GCF_002744715.1_ASM274471v1_genomic.fna.gz | prodigal -d GCF_002744715.1_ASM274471v1_genomic.fna/cds.fna -a GCF_002744715.1_ASM274471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,502] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,502] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,502] [INFO] Running command: hmmsearch --tblout GCF_002744715.1_ASM274471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/reference_markers.hmm GCF_002744715.1_ASM274471v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,834] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,836] [INFO] Found 6/6 markers.
[2024-01-24 13:40:41,882] [INFO] Query marker FASTA was written to GCF_002744715.1_ASM274471v1_genomic.fna/markers.fasta
[2024-01-24 13:40:41,883] [INFO] Task started: Blastn
[2024-01-24 13:40:41,883] [INFO] Running command: blastn -query GCF_002744715.1_ASM274471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/reference_markers.fasta -out GCF_002744715.1_ASM274471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,734] [INFO] Selected 18 target genomes.
[2024-01-24 13:40:42,734] [INFO] Target genome list was writen to GCF_002744715.1_ASM274471v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,739] [INFO] Task started: fastANI
[2024-01-24 13:40:42,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg42af6834-55e1-49a2-8b1d-3a151c1d0275/GCF_002744715.1_ASM274471v1_genomic.fna.gz --refList GCF_002744715.1_ASM274471v1_genomic.fna/target_genomes.txt --output GCF_002744715.1_ASM274471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:58,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:58,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:58,015] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:58,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:58,016] [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 profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	100.0	1330	1331	95	conclusive
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.7665	675	1331	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.4659	610	1331	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	80.1908	563	1331	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.1867	585	1331	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.8776	569	1331	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.7467	543	1331	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	79.725	458	1331	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.7215	446	1331	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.6874	532	1331	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	79.5596	610	1331	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.5522	587	1331	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.3719	515	1331	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.3201	552	1331	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	79.0297	439	1331	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	78.9417	462	1331	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.5673	441	1331	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.8202	180	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,018] [INFO] DFAST Taxonomy check result was written to GCF_002744715.1_ASM274471v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:58,018] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:58,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:58,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/checkm_data
[2024-01-24 13:40:58,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:58,065] [INFO] Task started: CheckM
[2024-01-24 13:40:58,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002744715.1_ASM274471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002744715.1_ASM274471v1_genomic.fna/checkm_input GCF_002744715.1_ASM274471v1_genomic.fna/checkm_result
[2024-01-24 13:41:36,572] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:36,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,598] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:36,599] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:36,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002744715.1_ASM274471v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:36,599] [INFO] Task started: Blastn
[2024-01-24 13:41:36,600] [INFO] Running command: blastn -query GCF_002744715.1_ASM274471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a83fd2c-4158-4dbc-b488-4a3183e08bbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002744715.1_ASM274471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,060] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,064] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:38,064] [INFO] Target genome list was writen to GCF_002744715.1_ASM274471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:38,074] [INFO] Task started: fastANI
[2024-01-24 13:41:38,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg42af6834-55e1-49a2-8b1d-3a151c1d0275/GCF_002744715.1_ASM274471v1_genomic.fna.gz --refList GCF_002744715.1_ASM274471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002744715.1_ASM274471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:50,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,476] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:50,477] [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_002744715.1	s__Marinobacter profundi	100.0	1330	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	conclusive
GCF_018424605.1	s__Marinobacter lipolyticus_B	80.8831	617	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.7721	674	1331	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	80.4634	609	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_008795955.1	s__Marinobacter sp008795955	80.1776	565	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018623515.1	s__Marinobacter sp018623515	80.1468	527	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	79.8693	442	1331	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	79.8676	570	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	79.7612	474	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000830985.1	s__Marinobacter similis	79.7326	544	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370345.1	s__Marinobacter sp008370345	79.7149	459	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	79.6778	533	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_000686085.1	s__Marinobacter sp000686085	79.4475	578	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005871205.1	s__Marinobacter alexandrii	79.2613	517	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_900114775.1	s__Marinobacter zhejiangensis	79.0297	439	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106945.1	s__Marinobacter mobilis	78.9612	460	1331	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 13:41:50,478] [INFO] GTDB search result was written to GCF_002744715.1_ASM274471v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:50,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:50,483] [INFO] DFAST_QC result json was written to GCF_002744715.1_ASM274471v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:50,483] [INFO] DFAST_QC completed!
[2024-01-24 13:41:50,483] [INFO] Total running time: 0h1m23s