[2024-01-24 14:14:00,819] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,821] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,821] [INFO] DQC Reference Directory: /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference
[2024-01-24 14:14:02,139] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,140] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,140] [INFO] Running command: gunzip -c /var/lib/cwl/stge667930c-5ae0-4c8a-a3a0-cf2d40f29f10/GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/cds.fna -a GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:17,304] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:17,304] [INFO] Task started: HMMsearch
[2024-01-24 14:14:17,304] [INFO] Running command: hmmsearch --tblout GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/reference_markers.hmm GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:17,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:17,842] [INFO] Found 6/6 markers.
[2024-01-24 14:14:17,911] [INFO] Query marker FASTA was written to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:17,912] [INFO] Task started: Blastn
[2024-01-24 14:14:17,912] [INFO] Running command: blastn -query GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/reference_markers.fasta -out GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:19,414] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:19,417] [INFO] Selected 23 target genomes.
[2024-01-24 14:14:19,418] [INFO] Target genome list was writen to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:19,427] [INFO] Task started: fastANI
[2024-01-24 14:14:19,428] [INFO] Running command: fastANI --query /var/lib/cwl/stge667930c-5ae0-4c8a-a3a0-cf2d40f29f10/GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna.gz --refList GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:43,798] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:43,798] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:43,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:43,819] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:14:43,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:14:43,820] [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
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	86.2372	904	1463	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	80.9868	685	1463	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	80.801	665	1463	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	80.7845	667	1463	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	80.5644	670	1463	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.5445	755	1463	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	80.473	669	1463	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	80.4112	663	1463	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.1971	635	1463	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.8911	633	1463	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.8181	546	1463	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.7999	580	1463	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.7436	653	1463	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.6355	561	1463	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.3933	588	1463	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.3452	545	1463	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.3325	538	1463	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	79.3209	520	1463	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	79.3117	527	1463	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.2915	494	1463	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	79.2116	506	1463	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.9691	556	1463	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.6067	342	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:43,821] [INFO] DFAST Taxonomy check result was written to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:14:43,822] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:43,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:43,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/checkm_data
[2024-01-24 14:14:43,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:43,874] [INFO] Task started: CheckM
[2024-01-24 14:14:43,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/checkm_input GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:28,118] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:28,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:28,146] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:28,146] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:28,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:28,147] [INFO] Task started: Blastn
[2024-01-24 14:15:28,147] [INFO] Running command: blastn -query GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg981d4692-cc5d-4800-803f-f79ea432f198/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:29,861] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:29,865] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:29,866] [INFO] Target genome list was writen to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:29,879] [INFO] Task started: fastANI
[2024-01-24 14:15:29,879] [INFO] Running command: fastANI --query /var/lib/cwl/stge667930c-5ae0-4c8a-a3a0-cf2d40f29f10/GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna.gz --refList GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:43,052] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:43,079] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:43,080] [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_900142185.1	s__Lutimaribacter pacificus	100.0	1463	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900100005.1	s__Lutimaribacter saemankumensis	86.2242	905	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	83.2979	858	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142665.1	s__Roseovarius pacificus	80.8127	664	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900109035.1	s__Cribrihabitans marinus	80.5433	672	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003344785.1	s__Puniceibacterium profundi	80.4095	659	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	80.2762	680	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.2511	666	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	79.8819	421	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	79.8472	652	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.3697	591	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054175.1	s__Allosediminivita pacifica	79.3228	526	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Allosediminivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	79.3098	541	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000473325.1	s__Leisingera caerulea	78.9493	559	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.5402	481	1463	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:43,082] [INFO] GTDB search result was written to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:43,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:43,088] [INFO] DFAST_QC result json was written to GCF_900142185.1_IMG-taxon_2695420927_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:15:43,088] [INFO] DFAST_QC completed!
[2024-01-24 14:15:43,088] [INFO] Total running time: 0h1m42s