[2024-01-24 13:49:54,849] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:54,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:54,851] [INFO] DQC Reference Directory: /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference
[2024-01-24 13:49:55,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:55,936] [INFO] Task started: Prodigal
[2024-01-24 13:49:55,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b8c13ce-ca93-4674-9568-af6832e91462/GCF_010671605.1_ASM1067160v1_genomic.fna.gz | prodigal -d GCF_010671605.1_ASM1067160v1_genomic.fna/cds.fna -a GCF_010671605.1_ASM1067160v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:08,995] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:08,995] [INFO] Task started: HMMsearch
[2024-01-24 13:50:08,995] [INFO] Running command: hmmsearch --tblout GCF_010671605.1_ASM1067160v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/reference_markers.hmm GCF_010671605.1_ASM1067160v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:09,222] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:09,223] [INFO] Found 6/6 markers.
[2024-01-24 13:50:09,256] [INFO] Query marker FASTA was written to GCF_010671605.1_ASM1067160v1_genomic.fna/markers.fasta
[2024-01-24 13:50:09,256] [INFO] Task started: Blastn
[2024-01-24 13:50:09,256] [INFO] Running command: blastn -query GCF_010671605.1_ASM1067160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/reference_markers.fasta -out GCF_010671605.1_ASM1067160v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:09,826] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:09,829] [INFO] Selected 26 target genomes.
[2024-01-24 13:50:09,829] [INFO] Target genome list was writen to GCF_010671605.1_ASM1067160v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:09,849] [INFO] Task started: fastANI
[2024-01-24 13:50:09,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8c13ce-ca93-4674-9568-af6832e91462/GCF_010671605.1_ASM1067160v1_genomic.fna.gz --refList GCF_010671605.1_ASM1067160v1_genomic.fna/target_genomes.txt --output GCF_010671605.1_ASM1067160v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:26,280] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:26,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:26,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:26,294] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:26,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:26,295] [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
Leptobacterium flavescens	strain=KCTC 22160	GCA_010671605.1	472055	472055	type	True	100.0	1402	1402	95	conclusive
Robertkochia marina	strain=CC-AMO-30D	GCA_007279605.1	1227945	1227945	type	True	77.4599	108	1402	95	below_threshold
Zhouia amylolytica	strain=CGMCC 1.6114	GCA_900116365.1	376730	376730	type	True	77.3938	90	1402	95	below_threshold
Robertkochia marina	strain=CC-AMO-30D	GCA_004799345.1	1227945	1227945	type	True	77.2914	106	1402	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.2678	93	1402	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	77.2382	111	1402	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.9783	98	1402	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.8943	93	1402	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.8618	72	1402	95	below_threshold
Sinomicrobium oceani	strain=CGMCC 1.12145	GCA_900119185.1	1150368	1150368	type	True	76.8295	92	1402	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	76.7859	63	1402	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	76.7326	81	1402	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_018863395.1	2842200	2842200	type	True	76.7288	93	1402	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.7082	75	1402	95	below_threshold
Sinomicrobium weinanense	strain=FJxs	GCA_014518365.1	2842200	2842200	type	True	76.6998	92	1402	95	below_threshold
Sinomicrobium pectinilyticum	strain=5DNS001	GCA_003725735.1	1084421	1084421	type	True	76.6545	105	1402	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	76.6294	73	1402	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.62	73	1402	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	76.4426	55	1402	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.4404	62	1402	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.3795	56	1402	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.3724	59	1402	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	76.3092	79	1402	95	below_threshold
Aestuariivivens sediminicola	strain=MTV5-3	GCA_022662015.1	2913560	2913560	type	True	76.1887	52	1402	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	75.9457	81	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:26,296] [INFO] DFAST Taxonomy check result was written to GCF_010671605.1_ASM1067160v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:26,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:26,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:26,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/checkm_data
[2024-01-24 13:50:26,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:26,337] [INFO] Task started: CheckM
[2024-01-24 13:50:26,337] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010671605.1_ASM1067160v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010671605.1_ASM1067160v1_genomic.fna/checkm_input GCF_010671605.1_ASM1067160v1_genomic.fna/checkm_result
[2024-01-24 13:51:04,885] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:04,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:04,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:04,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:04,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010671605.1_ASM1067160v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:04,901] [INFO] Task started: Blastn
[2024-01-24 13:51:04,901] [INFO] Running command: blastn -query GCF_010671605.1_ASM1067160v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgded0691d-96ce-495f-946a-80f7109e6a9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010671605.1_ASM1067160v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:05,713] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:05,715] [INFO] Selected 25 target genomes.
[2024-01-24 13:51:05,716] [INFO] Target genome list was writen to GCF_010671605.1_ASM1067160v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:05,727] [INFO] Task started: fastANI
[2024-01-24 13:51:05,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8c13ce-ca93-4674-9568-af6832e91462/GCF_010671605.1_ASM1067160v1_genomic.fna.gz --refList GCF_010671605.1_ASM1067160v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010671605.1_ASM1067160v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:22,100] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:22,114] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:22,114] [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_010671605.1	s__Leptobacterium flavescens	100.0	1402	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009901575.1	s__Leptobacterium sp009901575	77.4497	247	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leptobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116365.1	s__Zhouia amylolytica	77.346	88	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zhouia	95.0	98.62	98.62	0.95	0.95	2	-
GCF_004799345.1	s__Robertkochia marina	77.3078	103	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.2718	92	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300875.1	s__Galbibacter_B marinus	77.267	64	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786255.1	s__Robertkochia sp016786255	77.2165	111	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285545.1	s__Sinomicrobium sp003285545	76.9675	76	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	76.9298	87	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	76.8914	70	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119185.1	s__Sinomicrobium oceani	76.8295	92	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	76.7326	81	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863395.1	s__Sinomicrobium sp014518365	76.7288	93	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003725735.1	s__Sinomicrobium pectinilyticum	76.6545	105	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sinomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	76.6294	73	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_002150785.1	s__Arenibacter amylolyticus	76.5962	54	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.19	99.19	0.91	0.91	2	-
GCF_009735695.1	s__Gramella sp009735695	76.4144	84	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.4094	53	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	76.4014	54	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397005.1	s__Kordia aestuariivivens	76.3995	62	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.3543	56	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	76.3292	69	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626755.1	s__Ulvibacterium marinum	76.1057	52	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,115] [INFO] GTDB search result was written to GCF_010671605.1_ASM1067160v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:22,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:22,120] [INFO] DFAST_QC result json was written to GCF_010671605.1_ASM1067160v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:22,120] [INFO] DFAST_QC completed!
[2024-01-24 13:51:22,120] [INFO] Total running time: 0h1m27s