[2024-01-24 15:18:27,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,532] [INFO] DQC Reference Directory: /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference
[2024-01-24 15:18:28,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,956] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,956] [INFO] Running command: gunzip -c /var/lib/cwl/stg729dacdf-3ff3-4442-9112-f2c7581ac027/GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/cds.fna -a GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:44,474] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:44,475] [INFO] Task started: HMMsearch
[2024-01-24 15:18:44,475] [INFO] Running command: hmmsearch --tblout GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/reference_markers.hmm GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:44,790] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:44,791] [INFO] Found 6/6 markers.
[2024-01-24 15:18:44,836] [INFO] Query marker FASTA was written to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:18:44,837] [INFO] Task started: Blastn
[2024-01-24 15:18:44,837] [INFO] Running command: blastn -query GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/reference_markers.fasta -out GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:45,854] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:45,858] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:45,859] [INFO] Target genome list was writen to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:18:45,866] [INFO] Task started: fastANI
[2024-01-24 15:18:45,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg729dacdf-3ff3-4442-9112-f2c7581ac027/GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna.gz --refList GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:00,523] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:00,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:00,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:00,540] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:00,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:00,541] [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
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	100.0	1635	1639	95	conclusive
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	84.2835	975	1639	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	81.0141	773	1639	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	80.9035	772	1639	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.7601	710	1639	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.6632	721	1639	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.5861	735	1639	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	79.577	642	1639	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.6279	506	1639	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6272	422	1639	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.5418	377	1639	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.3114	425	1639	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.1177	370	1639	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6547	361	1639	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.6243	392	1639	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	76.8881	272	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:00,543] [INFO] DFAST Taxonomy check result was written to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:19:00,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:00,545] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:00,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/checkm_data
[2024-01-24 15:19:00,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:00,596] [INFO] Task started: CheckM
[2024-01-24 15:19:00,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/checkm_input GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:19:48,624] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:48,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:48,647] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:48,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:48,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:19:48,648] [INFO] Task started: Blastn
[2024-01-24 15:19:48,648] [INFO] Running command: blastn -query GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg299f6de8-5643-435a-9f2c-a4722f4255c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:50,276] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:50,279] [INFO] Selected 12 target genomes.
[2024-01-24 15:19:50,280] [INFO] Target genome list was writen to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:50,289] [INFO] Task started: fastANI
[2024-01-24 15:19:50,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg729dacdf-3ff3-4442-9112-f2c7581ac027/GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna.gz --refList GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:01,805] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:01,824] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:01,824] [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_900101475.1	s__Ruegeria_B marina	100.0	1634	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010500245.1	s__Ruegeria_B sp010500245	86.2837	1136	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	84.3068	972	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_005938215.1	s__Ruegeria sediminis	81.0311	771	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	80.912	771	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	80.751	711	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	80.603	733	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	80.5334	671	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013031405.1	s__Ruegeria sp013031405	80.4462	771	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	80.2179	639	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	79.7968	566	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	79.1458	586	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:01,826] [INFO] GTDB search result was written to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:01,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:01,831] [INFO] DFAST_QC result json was written to GCF_900101475.1_IMG-taxon_2617270884_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:20:01,831] [INFO] DFAST_QC completed!
[2024-01-24 15:20:01,831] [INFO] Total running time: 0h1m34s