[2024-01-24 13:25:29,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference
[2024-01-24 13:25:31,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,121] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg3eb0992b-25eb-4c93-8cc1-ad679418e81b/GCF_009669325.1_ASM966932v1_genomic.fna.gz | prodigal -d GCF_009669325.1_ASM966932v1_genomic.fna/cds.fna -a GCF_009669325.1_ASM966932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:42,920] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:42,920] [INFO] Task started: HMMsearch
[2024-01-24 13:25:42,920] [INFO] Running command: hmmsearch --tblout GCF_009669325.1_ASM966932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/reference_markers.hmm GCF_009669325.1_ASM966932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:43,190] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:43,191] [INFO] Found 6/6 markers.
[2024-01-24 13:25:43,231] [INFO] Query marker FASTA was written to GCF_009669325.1_ASM966932v1_genomic.fna/markers.fasta
[2024-01-24 13:25:43,231] [INFO] Task started: Blastn
[2024-01-24 13:25:43,231] [INFO] Running command: blastn -query GCF_009669325.1_ASM966932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/reference_markers.fasta -out GCF_009669325.1_ASM966932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:44,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:44,095] [INFO] Selected 19 target genomes.
[2024-01-24 13:25:44,095] [INFO] Target genome list was writen to GCF_009669325.1_ASM966932v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:44,102] [INFO] Task started: fastANI
[2024-01-24 13:25:44,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb0992b-25eb-4c93-8cc1-ad679418e81b/GCF_009669325.1_ASM966932v1_genomic.fna.gz --refList GCF_009669325.1_ASM966932v1_genomic.fna/target_genomes.txt --output GCF_009669325.1_ASM966932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:58,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:58,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:58,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:58,729] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:58,730] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:58,730] [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
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	100.0	1164	1165	95	conclusive
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	81.0549	639	1165	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	81.0424	638	1165	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.9675	575	1165	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	79.9274	578	1165	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.7882	596	1165	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	79.4838	558	1165	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	79.2485	586	1165	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.5497	414	1165	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.5309	396	1165	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	78.4173	413	1165	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	78.1566	353	1165	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.9149	398	1165	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7938	328	1165	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.5038	249	1165	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.4715	264	1165	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4611	271	1165	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.0754	244	1165	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.4846	113	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:58,732] [INFO] DFAST Taxonomy check result was written to GCF_009669325.1_ASM966932v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:58,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:58,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:58,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/checkm_data
[2024-01-24 13:25:58,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:58,781] [INFO] Task started: CheckM
[2024-01-24 13:25:58,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009669325.1_ASM966932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009669325.1_ASM966932v1_genomic.fna/checkm_input GCF_009669325.1_ASM966932v1_genomic.fna/checkm_result
[2024-01-24 13:26:37,365] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:37,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:37,390] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:37,391] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:37,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009669325.1_ASM966932v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:37,392] [INFO] Task started: Blastn
[2024-01-24 13:26:37,392] [INFO] Running command: blastn -query GCF_009669325.1_ASM966932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0375cca-efb1-41ea-a202-57a35c6acfad/dqc_reference/reference_markers_gtdb.fasta -out GCF_009669325.1_ASM966932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:38,749] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:38,753] [INFO] Selected 17 target genomes.
[2024-01-24 13:26:38,753] [INFO] Target genome list was writen to GCF_009669325.1_ASM966932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:38,772] [INFO] Task started: fastANI
[2024-01-24 13:26:38,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg3eb0992b-25eb-4c93-8cc1-ad679418e81b/GCF_009669325.1_ASM966932v1_genomic.fna.gz --refList GCF_009669325.1_ASM966932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009669325.1_ASM966932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:52,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:52,886] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:52,887] [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_009669325.1	s__Roseovarius bejariae	100.0	1164	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142665.1	s__Roseovarius pacificus	81.0425	638	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_900172255.1	s__Roseovarius halotolerans	79.9369	577	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142765.1	s__Roseovarius litoreus	79.7973	595	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_011601345.1	s__Roseovarius gahaiensis	79.4633	560	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	79.2423	588	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_002917925.1	s__Roseovarius confluentis	79.1954	523	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_009363715.1	s__Roseovarius sp009363715	79.1007	520	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.8801	498	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002166865.1	s__Roseovarius sp002166865	78.7545	504	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761875.1	s__Roseovarius aestuariivivens	78.6232	431	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	78.5596	413	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.47	422	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	78.4138	414	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	78.2983	410	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709405.1	s__Marinibacterium sp002709405	77.5634	341	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.0873	245	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:52,889] [INFO] GTDB search result was written to GCF_009669325.1_ASM966932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:52,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:52,895] [INFO] DFAST_QC result json was written to GCF_009669325.1_ASM966932v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:52,896] [INFO] DFAST_QC completed!
[2024-01-24 13:26:52,896] [INFO] Total running time: 0h1m23s