[2024-01-24 14:47:55,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,955] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,955] [INFO] DQC Reference Directory: /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference
[2024-01-24 14:47:58,523] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,525] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,525] [INFO] Running command: gunzip -c /var/lib/cwl/stgf88422df-1d4e-413e-ac27-06e7aa2ae96b/GCF_001020565.1_ASM102056v1_genomic.fna.gz | prodigal -d GCF_001020565.1_ASM102056v1_genomic.fna/cds.fna -a GCF_001020565.1_ASM102056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:17,475] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:17,476] [INFO] Task started: HMMsearch
[2024-01-24 14:48:17,476] [INFO] Running command: hmmsearch --tblout GCF_001020565.1_ASM102056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/reference_markers.hmm GCF_001020565.1_ASM102056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:17,798] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:17,799] [INFO] Found 6/6 markers.
[2024-01-24 14:48:17,845] [INFO] Query marker FASTA was written to GCF_001020565.1_ASM102056v1_genomic.fna/markers.fasta
[2024-01-24 14:48:17,846] [INFO] Task started: Blastn
[2024-01-24 14:48:17,846] [INFO] Running command: blastn -query GCF_001020565.1_ASM102056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/reference_markers.fasta -out GCF_001020565.1_ASM102056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:18,512] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:18,516] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:18,516] [INFO] Target genome list was writen to GCF_001020565.1_ASM102056v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:18,535] [INFO] Task started: fastANI
[2024-01-24 14:48:18,535] [INFO] Running command: fastANI --query /var/lib/cwl/stgf88422df-1d4e-413e-ac27-06e7aa2ae96b/GCF_001020565.1_ASM102056v1_genomic.fna.gz --refList GCF_001020565.1_ASM102056v1_genomic.fna/target_genomes.txt --output GCF_001020565.1_ASM102056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:33,672] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:33,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:33,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:33,690] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:33,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:33,691] [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
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	100.0	1349	1349	95	conclusive
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	78.1991	211	1349	95	below_threshold
Maribacter cobaltidurans	strain=B1	GCA_002269385.1	1178778	1178778	type	True	78.1273	359	1349	95	below_threshold
Maribacter cobaltidurans	strain=CGMCC 1.15508	GCA_014643435.1	1178778	1178778	type	True	78.0148	359	1349	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	78.0132	217	1349	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	77.7441	288	1349	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	77.7199	285	1349	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	77.7043	341	1349	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	77.6431	297	1349	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	77.5582	314	1349	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	77.4018	263	1349	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	77.3595	171	1349	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	77.0507	178	1349	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	76.9576	214	1349	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.8029	179	1349	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.7478	145	1349	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.686	156	1349	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.5143	73	1349	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	76.4231	163	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:33,696] [INFO] DFAST Taxonomy check result was written to GCF_001020565.1_ASM102056v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:33,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:33,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:33,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/checkm_data
[2024-01-24 14:48:33,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:33,745] [INFO] Task started: CheckM
[2024-01-24 14:48:33,746] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001020565.1_ASM102056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001020565.1_ASM102056v1_genomic.fna/checkm_input GCF_001020565.1_ASM102056v1_genomic.fna/checkm_result
[2024-01-24 14:49:25,658] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:25,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:25,682] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:25,682] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:25,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001020565.1_ASM102056v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:25,683] [INFO] Task started: Blastn
[2024-01-24 14:49:25,683] [INFO] Running command: blastn -query GCF_001020565.1_ASM102056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25139cfc-d17a-4973-91fa-312fba5cf234/dqc_reference/reference_markers_gtdb.fasta -out GCF_001020565.1_ASM102056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:26,510] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:26,513] [INFO] Selected 17 target genomes.
[2024-01-24 14:49:26,513] [INFO] Target genome list was writen to GCF_001020565.1_ASM102056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:26,531] [INFO] Task started: fastANI
[2024-01-24 14:49:26,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgf88422df-1d4e-413e-ac27-06e7aa2ae96b/GCF_001020565.1_ASM102056v1_genomic.fna.gz --refList GCF_001020565.1_ASM102056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001020565.1_ASM102056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:41,825] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:41,864] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:41,865] [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_001020565.1	s__Maribacter thermophilus	100.0	1349	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018100785.1	s__Maribacter sp018100785	90.0074	1203	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674825.1	s__Maribacter_A luteus	78.2101	211	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	78.0824	357	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000973105.1	s__Zobellia galactanivorans	78.0717	218	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_003970695.1	s__Maribacter sp002742365	78.0203	267	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_002742265.1	s__Maribacter sp002742265	77.7734	315	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188415.1	s__Maribacter sedimenticola	77.723	284	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
GCF_003933245.1	s__Maribacter algicola	77.7043	341	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	77.6327	298	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_003075045.1	s__Maribacter litoralis	77.5582	314	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_000621125.1	s__Maribacter antarcticus	77.4312	204	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	77.3961	262	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	77.3561	263	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	77.1476	283	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003149745.1	s__Muricauda koreensis	76.9159	115	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119145.1	s__Cellulophaga fucicola	76.773	131	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:41,867] [INFO] GTDB search result was written to GCF_001020565.1_ASM102056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:41,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:41,873] [INFO] DFAST_QC result json was written to GCF_001020565.1_ASM102056v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:41,874] [INFO] DFAST_QC completed!
[2024-01-24 14:49:41,874] [INFO] Total running time: 0h1m46s