[2024-01-24 14:46:55,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,459] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,459] [INFO] DQC Reference Directory: /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference
[2024-01-24 14:46:56,716] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:56,717] [INFO] Task started: Prodigal
[2024-01-24 14:46:56,717] [INFO] Running command: gunzip -c /var/lib/cwl/stgf55621fc-4c4e-491c-b9e5-4b32ae24b3e0/GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/cds.fna -a GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:10,421] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:10,422] [INFO] Task started: HMMsearch
[2024-01-24 14:47:10,422] [INFO] Running command: hmmsearch --tblout GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/reference_markers.hmm GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:10,741] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:10,742] [INFO] Found 6/6 markers.
[2024-01-24 14:47:10,778] [INFO] Query marker FASTA was written to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:10,779] [INFO] Task started: Blastn
[2024-01-24 14:47:10,779] [INFO] Running command: blastn -query GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/reference_markers.fasta -out GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,623] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,627] [INFO] Selected 14 target genomes.
[2024-01-24 14:47:11,627] [INFO] Target genome list was writen to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,653] [INFO] Task started: fastANI
[2024-01-24 14:47:11,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55621fc-4c4e-491c-b9e5-4b32ae24b3e0/GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna.gz --refList GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:24,542] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:24,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:24,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:24,554] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:47:24,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:24,555] [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
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	100.0	1336	1337	95	conclusive
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	99.9872	1313	1337	95	conclusive
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	99.9872	1313	1337	95	conclusive
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	82.1465	855	1337	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	82.1224	844	1337	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	82.0899	847	1337	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	81.9706	829	1337	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	81.2701	781	1337	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	79.9756	659	1337	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.4276	514	1337	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.7736	330	1337	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.702	355	1337	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.5046	341	1337	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	77.2862	191	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:24,556] [INFO] DFAST Taxonomy check result was written to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:47:24,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:24,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:24,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/checkm_data
[2024-01-24 14:47:24,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:24,602] [INFO] Task started: CheckM
[2024-01-24 14:47:24,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/checkm_input GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:48:08,865] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:08,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:08,886] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:08,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:08,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:48:08,887] [INFO] Task started: Blastn
[2024-01-24 14:48:08,887] [INFO] Running command: blastn -query GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg62109639-442b-4be4-bd3e-b2e9c64ded21/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:10,171] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:10,181] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:10,181] [INFO] Target genome list was writen to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:10,192] [INFO] Task started: fastANI
[2024-01-24 14:48:10,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgf55621fc-4c4e-491c-b9e5-4b32ae24b3e0/GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna.gz --refList GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:22,441] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:22,452] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:22,452] [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_001258055.1	s__Phaeobacter italicus	99.9872	1313	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	conclusive
GCF_002407245.1	s__Phaeobacter piscinae	82.1507	854	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	82.1486	840	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000473105.1	s__Phaeobacter inhibens	81.9706	829	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.82	97.14	0.94	0.90	26	-
GCF_001888185.1	s__Phaeobacter porticola	81.2701	781	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	80.2891	609	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	80.1965	580	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	80.1092	580	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	80.0797	674	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_001679925.1	s__Leisingera sp001679925	80.0267	623	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	80.0105	642	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_000473325.1	s__Leisingera caerulea	79.9711	660	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884385.1	s__Pseudophaeobacter_A sp014884385	79.6072	544	1337	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	99.80	99.80	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:22,454] [INFO] GTDB search result was written to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:22,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:22,458] [INFO] DFAST_QC result json was written to GCF_900113345.1_IMG-taxon_2622736589_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:48:22,459] [INFO] DFAST_QC completed!
[2024-01-24 14:48:22,459] [INFO] Total running time: 0h1m27s