[2023-06-27 14:44:02,646] [INFO] DFAST_QC pipeline started.
[2023-06-27 14:44:02,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 14:44:02,648] [INFO] DQC Reference Directory: /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference
[2023-06-27 14:44:04,510] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 14:44:04,511] [INFO] Task started: Prodigal
[2023-06-27 14:44:04,511] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc3f8fdf-be20-4619-90a1-ca87817f5f41/GCA_002709085.1_ASM270908v1_genomic.fna.gz | prodigal -d GCA_002709085.1_ASM270908v1_genomic.fna/cds.fna -a GCA_002709085.1_ASM270908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 14:44:13,953] [INFO] Task succeeded: Prodigal
[2023-06-27 14:44:13,954] [INFO] Task started: HMMsearch
[2023-06-27 14:44:13,954] [INFO] Running command: hmmsearch --tblout GCA_002709085.1_ASM270908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/reference_markers.hmm GCA_002709085.1_ASM270908v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 14:44:14,248] [INFO] Task succeeded: HMMsearch
[2023-06-27 14:44:14,250] [INFO] Found 6/6 markers.
[2023-06-27 14:44:14,282] [INFO] Query marker FASTA was written to GCA_002709085.1_ASM270908v1_genomic.fna/markers.fasta
[2023-06-27 14:44:14,283] [INFO] Task started: Blastn
[2023-06-27 14:44:14,283] [INFO] Running command: blastn -query GCA_002709085.1_ASM270908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/reference_markers.fasta -out GCA_002709085.1_ASM270908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:44:15,277] [INFO] Task succeeded: Blastn
[2023-06-27 14:44:15,283] [INFO] Selected 23 target genomes.
[2023-06-27 14:44:15,283] [INFO] Target genome list was writen to GCA_002709085.1_ASM270908v1_genomic.fna/target_genomes.txt
[2023-06-27 14:44:15,297] [INFO] Task started: fastANI
[2023-06-27 14:44:15,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc3f8fdf-be20-4619-90a1-ca87817f5f41/GCA_002709085.1_ASM270908v1_genomic.fna.gz --refList GCA_002709085.1_ASM270908v1_genomic.fna/target_genomes.txt --output GCA_002709085.1_ASM270908v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 14:44:32,856] [INFO] Task succeeded: fastANI
[2023-06-27 14:44:32,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 14:44:32,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 14:44:32,881] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 14:44:32,881] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 14:44:32,882] [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
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.5051	478	967	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	79.4084	461	967	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.4075	462	967	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.3028	348	967	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.2867	356	967	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.2239	273	967	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.0326	280	967	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.0072	283	967	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	77.9396	272	967	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.8946	314	967	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.8576	286	967	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.8387	283	967	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.8322	286	967	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7978	251	967	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.7767	273	967	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.5552	243	967	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.4954	214	967	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.4453	255	967	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.1566	210	967	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.9725	185	967	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.9128	189	967	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.8058	189	967	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7523	127	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 14:44:32,892] [INFO] DFAST Taxonomy check result was written to GCA_002709085.1_ASM270908v1_genomic.fna/tc_result.tsv
[2023-06-27 14:44:32,893] [INFO] ===== Taxonomy check completed =====
[2023-06-27 14:44:32,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 14:44:32,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/checkm_data
[2023-06-27 14:44:32,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 14:44:32,936] [INFO] Task started: CheckM
[2023-06-27 14:44:32,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002709085.1_ASM270908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002709085.1_ASM270908v1_genomic.fna/checkm_input GCA_002709085.1_ASM270908v1_genomic.fna/checkm_result
[2023-06-27 14:45:04,628] [INFO] Task succeeded: CheckM
[2023-06-27 14:45:04,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 14:45:04,655] [INFO] ===== Completeness check finished =====
[2023-06-27 14:45:04,656] [INFO] ===== Start GTDB Search =====
[2023-06-27 14:45:04,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002709085.1_ASM270908v1_genomic.fna/markers.fasta)
[2023-06-27 14:45:04,656] [INFO] Task started: Blastn
[2023-06-27 14:45:04,657] [INFO] Running command: blastn -query GCA_002709085.1_ASM270908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge063ff46-709b-4974-a1c7-8bacf3574742/dqc_reference/reference_markers_gtdb.fasta -out GCA_002709085.1_ASM270908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 14:45:06,186] [INFO] Task succeeded: Blastn
[2023-06-27 14:45:06,191] [INFO] Selected 15 target genomes.
[2023-06-27 14:45:06,191] [INFO] Target genome list was writen to GCA_002709085.1_ASM270908v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 14:45:06,204] [INFO] Task started: fastANI
[2023-06-27 14:45:06,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc3f8fdf-be20-4619-90a1-ca87817f5f41/GCA_002709085.1_ASM270908v1_genomic.fna.gz --refList GCA_002709085.1_ASM270908v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002709085.1_ASM270908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 14:45:17,566] [INFO] Task succeeded: fastANI
[2023-06-27 14:45:17,586] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 14:45:17,586] [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
GCA_002709085.1	s__Pseudooceanicola sp002709085	100.0	961	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014638275.1	s__Pseudooceanicola flagellatus	79.6636	492	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.5051	478	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	79.4869	470	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	79.4134	461	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	79.3221	476	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.2712	351	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003590145.2	s__Pseudooceanicola algae	78.2503	271	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.2358	316	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003575965.1	s__Pseudooceanicola sediminis	77.9778	269	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
GCF_900109145.1	s__Marinovum algicola	77.9616	301	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_010614805.1	s__Pseudooceanicola sp010614805	77.8837	315	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	77.8266	284	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.6623	273	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	77.6535	273	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 14:45:17,588] [INFO] GTDB search result was written to GCA_002709085.1_ASM270908v1_genomic.fna/result_gtdb.tsv
[2023-06-27 14:45:17,589] [INFO] ===== GTDB Search completed =====
[2023-06-27 14:45:17,593] [INFO] DFAST_QC result json was written to GCA_002709085.1_ASM270908v1_genomic.fna/dqc_result.json
[2023-06-27 14:45:17,593] [INFO] DFAST_QC completed!
[2023-06-27 14:45:17,593] [INFO] Total running time: 0h1m15s