[2024-01-24 13:22:31,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference
[2024-01-24 13:22:32,410] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,410] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,411] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbaac53d-26b7-467b-b5e3-d0fb9ea2fa65/GCF_019312585.1_ASM1931258v1_genomic.fna.gz | prodigal -d GCF_019312585.1_ASM1931258v1_genomic.fna/cds.fna -a GCF_019312585.1_ASM1931258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:43,490] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:43,491] [INFO] Task started: HMMsearch
[2024-01-24 13:22:43,491] [INFO] Running command: hmmsearch --tblout GCF_019312585.1_ASM1931258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/reference_markers.hmm GCF_019312585.1_ASM1931258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:43,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:43,764] [INFO] Found 6/6 markers.
[2024-01-24 13:22:43,791] [INFO] Query marker FASTA was written to GCF_019312585.1_ASM1931258v1_genomic.fna/markers.fasta
[2024-01-24 13:22:43,791] [INFO] Task started: Blastn
[2024-01-24 13:22:43,791] [INFO] Running command: blastn -query GCF_019312585.1_ASM1931258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/reference_markers.fasta -out GCF_019312585.1_ASM1931258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:44,431] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:44,435] [INFO] Selected 27 target genomes.
[2024-01-24 13:22:44,436] [INFO] Target genome list was writen to GCF_019312585.1_ASM1931258v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:47,180] [INFO] Task started: fastANI
[2024-01-24 13:22:47,181] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbaac53d-26b7-467b-b5e3-d0fb9ea2fa65/GCF_019312585.1_ASM1931258v1_genomic.fna.gz --refList GCF_019312585.1_ASM1931258v1_genomic.fna/target_genomes.txt --output GCF_019312585.1_ASM1931258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:01,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:01,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:01,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:01,957] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:01,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:01,958] [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
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	100.0	979	979	95	conclusive
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2473	92	979	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.036	195	979	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.0255	92	979	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.9922	87	979	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.9757	193	979	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.9729	132	979	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.933	50	979	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.8995	75	979	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	76.8905	95	979	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.8886	124	979	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.8815	130	979	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.8595	143	979	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	76.8376	81	979	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.8193	81	979	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7744	84	979	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.7535	167	979	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.7367	90	979	95	below_threshold
Aquimarina agarilytica	strain=ZC1	GCA_000255455.1	1087449	1087449	type	True	76.7188	62	979	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	76.6732	97	979	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	76.6223	60	979	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	76.5973	107	979	95	below_threshold
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	76.5387	69	979	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	76.4802	96	979	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	75.9925	55	979	95	below_threshold
Flavobacterium aquatile	strain=ATCC 11947	GCA_002217235.1	245	245	type	True	75.9396	53	979	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,959] [INFO] DFAST Taxonomy check result was written to GCF_019312585.1_ASM1931258v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:01,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:01,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:01,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/checkm_data
[2024-01-24 13:23:01,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:01,993] [INFO] Task started: CheckM
[2024-01-24 13:23:01,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019312585.1_ASM1931258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019312585.1_ASM1931258v1_genomic.fna/checkm_input GCF_019312585.1_ASM1931258v1_genomic.fna/checkm_result
[2024-01-24 13:23:37,616] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:37,617] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:37,639] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:37,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:37,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019312585.1_ASM1931258v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:37,641] [INFO] Task started: Blastn
[2024-01-24 13:23:37,641] [INFO] Running command: blastn -query GCF_019312585.1_ASM1931258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc26cb97-4b8e-44e6-91fb-890590533102/dqc_reference/reference_markers_gtdb.fasta -out GCF_019312585.1_ASM1931258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:38,569] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:38,573] [INFO] Selected 23 target genomes.
[2024-01-24 13:23:38,574] [INFO] Target genome list was writen to GCF_019312585.1_ASM1931258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:38,944] [INFO] Task started: fastANI
[2024-01-24 13:23:38,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbaac53d-26b7-467b-b5e3-d0fb9ea2fa65/GCF_019312585.1_ASM1931258v1_genomic.fna.gz --refList GCF_019312585.1_ASM1931258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019312585.1_ASM1931258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:50,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:50,901] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:23:50,901] [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_002694465.1	s__IN17 sp002694465	94.4851	828	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002707025.1	s__IN17 sp002707025	77.3349	266	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCF_002813135.1	s__Altibacter sp002813135	77.1809	193	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	77.1648	132	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_013002065.1	s__SMXJ01 sp013002065	77.1552	159	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	77.0305	157	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.9969	168	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.9833	103	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	76.974	106	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.9636	194	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_006346335.1	s__Aequorivita sinensis	76.9376	134	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_014641635.1	s__Aquaticitalea lipolytica	76.9361	92	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	76.8815	130	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688405.1	s__Ulvibacter antarcticus	76.8595	143	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	76.8472	151	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.7529	167	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.5978	102	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429125.1	s__Aequorivita capsosiphonis	76.5973	107	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.3541	110	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003650305.1	s__PRS1 sp003650305	76.2378	84	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.0029	92	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	75.9925	55	979	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,903] [INFO] GTDB search result was written to GCF_019312585.1_ASM1931258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:50,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:50,908] [INFO] DFAST_QC result json was written to GCF_019312585.1_ASM1931258v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:50,908] [INFO] DFAST_QC completed!
[2024-01-24 13:23:50,908] [INFO] Total running time: 0h1m20s