[2023-06-19 11:45:53,982] [INFO] DFAST_QC pipeline started.
[2023-06-19 11:45:53,984] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 11:45:53,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference
[2023-06-19 11:45:55,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 11:45:55,735] [INFO] Task started: Prodigal
[2023-06-19 11:45:55,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg80cd26d3-3501-4ddd-8f10-cb495c139a05/GCA_018679595.1_ASM1867959v1_genomic.fna.gz | prodigal -d GCA_018679595.1_ASM1867959v1_genomic.fna/cds.fna -a GCA_018679595.1_ASM1867959v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 11:46:06,392] [INFO] Task succeeded: Prodigal
[2023-06-19 11:46:06,392] [INFO] Task started: HMMsearch
[2023-06-19 11:46:06,392] [INFO] Running command: hmmsearch --tblout GCA_018679595.1_ASM1867959v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/reference_markers.hmm GCA_018679595.1_ASM1867959v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 11:46:06,623] [INFO] Task succeeded: HMMsearch
[2023-06-19 11:46:06,625] [INFO] Found 6/6 markers.
[2023-06-19 11:46:06,655] [INFO] Query marker FASTA was written to GCA_018679595.1_ASM1867959v1_genomic.fna/markers.fasta
[2023-06-19 11:46:06,655] [INFO] Task started: Blastn
[2023-06-19 11:46:06,655] [INFO] Running command: blastn -query GCA_018679595.1_ASM1867959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/reference_markers.fasta -out GCA_018679595.1_ASM1867959v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:46:07,306] [INFO] Task succeeded: Blastn
[2023-06-19 11:46:07,310] [INFO] Selected 32 target genomes.
[2023-06-19 11:46:07,310] [INFO] Target genome list was writen to GCA_018679595.1_ASM1867959v1_genomic.fna/target_genomes.txt
[2023-06-19 11:46:07,318] [INFO] Task started: fastANI
[2023-06-19 11:46:07,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cd26d3-3501-4ddd-8f10-cb495c139a05/GCA_018679595.1_ASM1867959v1_genomic.fna.gz --refList GCA_018679595.1_ASM1867959v1_genomic.fna/target_genomes.txt --output GCA_018679595.1_ASM1867959v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 11:46:30,561] [INFO] Task succeeded: fastANI
[2023-06-19 11:46:30,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 11:46:30,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 11:46:30,587] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 11:46:30,587] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 11:46:30,587] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.2236	151	906	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.9726	147	906	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.8955	105	906	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.8845	146	906	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.8494	142	906	95	below_threshold
Gelidibacter algens	strain=DSM 12408	GCA_003259265.1	49280	49280	type	True	76.8484	91	906	95	below_threshold
Gelidibacter algens	strain=ACAM 536	GCA_001678675.1	49280	49280	type	True	76.8456	89	906	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.8443	130	906	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.8067	101	906	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.7986	110	906	95	below_threshold
Hyunsoonleella pacifica	strain=CGMCC 1.11009	GCA_014636335.1	1080224	1080224	type	True	76.7353	102	906	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.7353	102	906	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.6693	108	906	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.6613	115	906	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.629	131	906	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.6273	157	906	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	76.6005	105	906	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.5937	124	906	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	76.5917	102	906	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5853	138	906	95	below_threshold
Tamlana crocina	strain=HST1-43	GCA_012037625.1	393006	393006	type	True	76.5783	82	906	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.5681	115	906	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	76.55	106	906	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.5204	117	906	95	below_threshold
Gelidibacter pelagius	strain=DF109	GCA_017581925.1	2819985	2819985	type	True	76.4895	103	906	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.4162	113	906	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	76.4092	108	906	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.3515	81	906	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	76.3491	98	906	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.3395	126	906	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	76.3315	114	906	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.3254	110	906	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 11:46:30,590] [INFO] DFAST Taxonomy check result was written to GCA_018679595.1_ASM1867959v1_genomic.fna/tc_result.tsv
[2023-06-19 11:46:30,591] [INFO] ===== Taxonomy check completed =====
[2023-06-19 11:46:30,591] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 11:46:30,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/checkm_data
[2023-06-19 11:46:30,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 11:46:30,626] [INFO] Task started: CheckM
[2023-06-19 11:46:30,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018679595.1_ASM1867959v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018679595.1_ASM1867959v1_genomic.fna/checkm_input GCA_018679595.1_ASM1867959v1_genomic.fna/checkm_result
[2023-06-19 11:47:06,465] [INFO] Task succeeded: CheckM
[2023-06-19 11:47:06,466] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 11:47:06,484] [INFO] ===== Completeness check finished =====
[2023-06-19 11:47:06,484] [INFO] ===== Start GTDB Search =====
[2023-06-19 11:47:06,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018679595.1_ASM1867959v1_genomic.fna/markers.fasta)
[2023-06-19 11:47:06,485] [INFO] Task started: Blastn
[2023-06-19 11:47:06,485] [INFO] Running command: blastn -query GCA_018679595.1_ASM1867959v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb1d436-1189-4cbd-a93b-29ae46b82855/dqc_reference/reference_markers_gtdb.fasta -out GCA_018679595.1_ASM1867959v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 11:47:07,443] [INFO] Task succeeded: Blastn
[2023-06-19 11:47:07,448] [INFO] Selected 25 target genomes.
[2023-06-19 11:47:07,448] [INFO] Target genome list was writen to GCA_018679595.1_ASM1867959v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 11:47:07,481] [INFO] Task started: fastANI
[2023-06-19 11:47:07,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg80cd26d3-3501-4ddd-8f10-cb495c139a05/GCA_018679595.1_ASM1867959v1_genomic.fna.gz --refList GCA_018679595.1_ASM1867959v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018679595.1_ASM1867959v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 11:47:24,441] [INFO] Task succeeded: fastANI
[2023-06-19 11:47:24,463] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 11:47:24,464] [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_013001285.1	s__SHLJ01 sp004283005	99.7299	862	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SHLJ01	95.0	99.69	99.59	0.94	0.91	6	conclusive
GCA_013001965.1	s__SHLJ01 sp013001965	77.4739	242	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SHLJ01	95.0	99.22	99.22	0.91	0.91	2	-
GCF_005047595.1	s__CAU-1491 sp005047595	77.2236	151	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.1532	143	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	77.14	94	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.0956	142	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCA_003650305.1	s__PRS1 sp003650305	77.0747	146	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	77.0567	98	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643165.1	s__Psychroserpens sp017643165	76.8599	111	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.99	99.97	1.00	1.00	7	-
GCF_018860545.1	s__Winogradskyella psychrotolerans_A	76.851	103	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	76.8015	135	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	76.7986	110	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	76.7909	123	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	76.7369	103	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002428965.1	s__Jejuia sp002428965	76.6941	99	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	76.6693	108	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_900112595.1	s__Algibacter_B pectinivorans	76.6613	115	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	76.5943	155	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895005.1	s__Hanstruepera neustonica	76.5937	124	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	76.5357	122	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017581925.1	s__Gelidibacter sp017581925	76.4895	103	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	76.4557	136	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	76.4028	147	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004115975.1	s__Gelidibacter gilvus	76.3491	98	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394655.1	s__Winogradskyella schleiferi	76.3315	114	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 11:47:24,466] [INFO] GTDB search result was written to GCA_018679595.1_ASM1867959v1_genomic.fna/result_gtdb.tsv
[2023-06-19 11:47:24,466] [INFO] ===== GTDB Search completed =====
[2023-06-19 11:47:24,471] [INFO] DFAST_QC result json was written to GCA_018679595.1_ASM1867959v1_genomic.fna/dqc_result.json
[2023-06-19 11:47:24,472] [INFO] DFAST_QC completed!
[2023-06-19 11:47:24,472] [INFO] Total running time: 0h1m30s