[2024-01-24 13:13:00,965] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:00,967] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:00,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference
[2024-01-24 13:13:02,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:02,161] [INFO] Task started: Prodigal
[2024-01-24 13:13:02,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg8de45057-0b14-433b-970e-498c521f4425/GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/cds.fna -a GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:14,611] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:14,611] [INFO] Task started: HMMsearch
[2024-01-24 13:13:14,611] [INFO] Running command: hmmsearch --tblout GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/reference_markers.hmm GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:14,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:14,942] [INFO] Found 6/6 markers.
[2024-01-24 13:13:14,975] [INFO] Query marker FASTA was written to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:14,975] [INFO] Task started: Blastn
[2024-01-24 13:13:14,975] [INFO] Running command: blastn -query GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/reference_markers.fasta -out GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:15,690] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:15,693] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:15,694] [INFO] Target genome list was writen to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:15,784] [INFO] Task started: fastANI
[2024-01-24 13:13:15,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de45057-0b14-433b-970e-498c521f4425/GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna.gz --refList GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:29,126] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:29,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:29,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:29,140] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:29,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:29,141] [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
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	100.0	1316	1319	95	conclusive
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	99.9847	1306	1319	95	conclusive
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	78.1418	319	1319	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	77.9345	329	1319	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.779	268	1319	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	77.7373	255	1319	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.69	256	1319	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.5902	232	1319	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	77.5603	237	1319	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4648	245	1319	95	below_threshold
Shimia abyssi	strain=DSM 100673	GCA_003014475.1	1662395	1662395	type	True	77.4519	122	1319	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.3526	141	1319	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.3376	182	1319	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.3121	183	1319	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	77.1731	108	1319	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.9998	72	1319	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	76.9982	117	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:29,142] [INFO] DFAST Taxonomy check result was written to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:29,143] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:29,143] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:29,143] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/checkm_data
[2024-01-24 13:13:29,145] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:29,190] [INFO] Task started: CheckM
[2024-01-24 13:13:29,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/checkm_input GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:14:11,052] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:11,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:11,071] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:11,072] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:11,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:14:11,072] [INFO] Task started: Blastn
[2024-01-24 13:14:11,073] [INFO] Running command: blastn -query GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0864f08a-ec83-40d6-ae23-f37500f12592/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:12,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:12,197] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:12,197] [INFO] Target genome list was writen to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:12,309] [INFO] Task started: fastANI
[2024-01-24 13:14:12,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg8de45057-0b14-433b-970e-498c521f4425/GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna.gz --refList GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:26,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:26,098] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:26,099] [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_900102795.1	s__Epibacterium ulvae	100.0	1316	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_009617595.1	s__Epibacterium aquimaris	78.1418	319	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018678075.1	s__Epibacterium ulvae_A	78.0725	326	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009496005.1	s__Epibacterium litoralis	77.9451	328	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678945.1	s__Pseudophaeobacter_A gallaeciensis_A	77.807	235	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001458415.1	s__Epibacterium multivorans	77.7661	269	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	77.7637	255	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_014884385.1	s__Pseudophaeobacter_A sp014884385	77.7434	196	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter_A	95.0	99.80	99.80	0.96	0.96	2	-
GCF_900313025.1	s__Pseudophaeobacter sp900313025	77.713	258	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	77.6711	218	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.5989	234	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.5789	224	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002087335.1	s__Pseudophaeobacter leonis	77.5603	237	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004123675.1	s__Leisingera sp004123675	77.5136	227	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_000813965.1	s__Leisingera sp000813965	77.5134	214	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014475.1	s__Shimia abyssi	77.4254	123	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114415.1	s__Shimia haliotis	77.32	144	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184935.1	s__Actibacterium_A lipolyticum	76.9982	117	1319	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:26,100] [INFO] GTDB search result was written to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:26,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:26,105] [INFO] DFAST_QC result json was written to GCF_900102795.1_IMG-taxon_2622736501_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:26,106] [INFO] DFAST_QC completed!
[2024-01-24 13:14:26,106] [INFO] Total running time: 0h1m25s