[2024-01-25 17:36:20,626] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:36:20,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:36:20,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference
[2024-01-25 17:36:21,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:36:21,875] [INFO] Task started: Prodigal
[2024-01-25 17:36:21,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg72898472-0332-4525-ac76-e8002b3082ec/GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/cds.fna -a GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:36:32,340] [INFO] Task succeeded: Prodigal
[2024-01-25 17:36:32,340] [INFO] Task started: HMMsearch
[2024-01-25 17:36:32,340] [INFO] Running command: hmmsearch --tblout GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/reference_markers.hmm GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:36:32,573] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:36:32,574] [INFO] Found 6/6 markers.
[2024-01-25 17:36:32,604] [INFO] Query marker FASTA was written to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:36:32,605] [INFO] Task started: Blastn
[2024-01-25 17:36:32,605] [INFO] Running command: blastn -query GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/reference_markers.fasta -out GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:33,430] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:33,439] [INFO] Selected 16 target genomes.
[2024-01-25 17:36:33,439] [INFO] Target genome list was writen to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:36:33,455] [INFO] Task started: fastANI
[2024-01-25 17:36:33,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg72898472-0332-4525-ac76-e8002b3082ec/GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna.gz --refList GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:48,453] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:48,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:48,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:48,464] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:48,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:48,465] [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 gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	100.0	1276	1276	95	conclusive
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	82.4001	887	1276	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	82.1721	829	1276	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	82.1315	834	1276	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	82.0002	846	1276	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	81.8346	854	1276	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	81.3731	813	1276	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	81.243	681	1276	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.6545	743	1276	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.4074	633	1276	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.3022	644	1276	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.2784	607	1276	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	80.0596	611	1276	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.9966	578	1276	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	79.8495	581	1276	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.2647	507	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:48,480] [INFO] DFAST Taxonomy check result was written to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:36:48,481] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:48,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:48,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/checkm_data
[2024-01-25 17:36:48,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:48,530] [INFO] Task started: CheckM
[2024-01-25 17:36:48,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/checkm_input GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:37:21,677] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:21,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:21,699] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:21,699] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:21,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:37:21,699] [INFO] Task started: Blastn
[2024-01-25 17:37:21,700] [INFO] Running command: blastn -query GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ccda5da-9b8f-4102-9d1d-b24516d79cf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:23,330] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:23,333] [INFO] Selected 18 target genomes.
[2024-01-25 17:37:23,333] [INFO] Target genome list was writen to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:23,342] [INFO] Task started: fastANI
[2024-01-25 17:37:23,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg72898472-0332-4525-ac76-e8002b3082ec/GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna.gz --refList GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:38,731] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:38,741] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:38,742] [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_900115175.1	s__Marinobacter gudaonensis	100.0	1276	1276	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_002933275.1	s__Marinobacter maroccanus	82.396	888	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617755.1	s__Marinobacter salsuginis	82.2455	854	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
GCF_001650915.1	s__Marinobacter sp001650915	82.2141	896	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_002933295.1	s__Marinobacter flavimaris	82.1339	833	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	82.0447	833	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCA_003030785.1	s__Marinobacter sp003030785	82.0382	511	1276	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	82.0064	845	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_008107725.1	s__Marinobacter sp008107725	81.9486	827	1276	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	81.8577	851	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_900188435.1	s__Marinobacter sp900188435	81.7369	806	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441595.1	s__Marinobacter sp003441595	81.7097	789	1276	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	81.2435	680	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	81.1858	697	1276	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	80.8742	564	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	80.6673	662	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707215.1	s__Marinobacter sp002707215	80.6187	422	1276	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	80.3198	642	1276	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:38,745] [INFO] GTDB search result was written to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:38,746] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:38,762] [INFO] DFAST_QC result json was written to GCF_900115175.1_IMG-taxon_2617270919_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:37:38,763] [INFO] DFAST_QC completed!
[2024-01-25 17:37:38,763] [INFO] Total running time: 0h1m18s