[2024-01-25 17:50:50,629] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:50,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:50,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference
[2024-01-25 17:50:51,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:51,752] [INFO] Task started: Prodigal
[2024-01-25 17:50:51,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg69a8fe3a-21f3-4989-89b1-ab6f85b554c9/GCF_023634845.1_ASM2363484v1_genomic.fna.gz | prodigal -d GCF_023634845.1_ASM2363484v1_genomic.fna/cds.fna -a GCF_023634845.1_ASM2363484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:06,302] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:06,302] [INFO] Task started: HMMsearch
[2024-01-25 17:51:06,302] [INFO] Running command: hmmsearch --tblout GCF_023634845.1_ASM2363484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/reference_markers.hmm GCF_023634845.1_ASM2363484v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:06,537] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:06,538] [INFO] Found 6/6 markers.
[2024-01-25 17:51:06,580] [INFO] Query marker FASTA was written to GCF_023634845.1_ASM2363484v1_genomic.fna/markers.fasta
[2024-01-25 17:51:06,580] [INFO] Task started: Blastn
[2024-01-25 17:51:06,580] [INFO] Running command: blastn -query GCF_023634845.1_ASM2363484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/reference_markers.fasta -out GCF_023634845.1_ASM2363484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:07,233] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:07,236] [INFO] Selected 21 target genomes.
[2024-01-25 17:51:07,236] [INFO] Target genome list was writen to GCF_023634845.1_ASM2363484v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:07,255] [INFO] Task started: fastANI
[2024-01-25 17:51:07,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a8fe3a-21f3-4989-89b1-ab6f85b554c9/GCF_023634845.1_ASM2363484v1_genomic.fna.gz --refList GCF_023634845.1_ASM2363484v1_genomic.fna/target_genomes.txt --output GCF_023634845.1_ASM2363484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:21,454] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:21,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:21,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:21,466] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:21,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:21,467] [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
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	100.0	1378	1404	95	conclusive
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	79.6295	398	1404	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	78.829	343	1404	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	78.179	183	1404	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	77.7937	250	1404	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.7642	184	1404	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	77.6708	252	1404	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	77.6214	199	1404	95	below_threshold
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	77.6122	185	1404	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	77.5269	185	1404	95	below_threshold
Flavobacterium daejeonense	strain=DSM 17708	GCA_000425425.1	350893	350893	type	True	77.4503	160	1404	95	below_threshold
Flavobacterium johnsoniae	strain=UW101; ATCC 17061	GCA_000016645.1	986	986	type	True	77.3511	187	1404	95	below_threshold
Flavobacterium johnsoniae	strain=DSM 2064	GCA_900142355.1	986	986	type	True	77.2824	183	1404	95	below_threshold
Flavobacterium johnsoniae	strain=ATCC 17061	GCA_002221975.1	986	986	type	True	77.2507	176	1404	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.2451	174	1404	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	77.1976	149	1404	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	77.1963	163	1404	95	below_threshold
Flavobacterium beibuense	strain=F44-8	GCA_000769915.1	657326	657326	type	True	76.9793	120	1404	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.6087	55	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:21,468] [INFO] DFAST Taxonomy check result was written to GCF_023634845.1_ASM2363484v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:21,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:21,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:21,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/checkm_data
[2024-01-25 17:51:21,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:21,512] [INFO] Task started: CheckM
[2024-01-25 17:51:21,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023634845.1_ASM2363484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023634845.1_ASM2363484v1_genomic.fna/checkm_input GCF_023634845.1_ASM2363484v1_genomic.fna/checkm_result
[2024-01-25 17:52:04,880] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:04,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:04,904] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:04,904] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:04,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023634845.1_ASM2363484v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:04,905] [INFO] Task started: Blastn
[2024-01-25 17:52:04,906] [INFO] Running command: blastn -query GCF_023634845.1_ASM2363484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1f8d87a-6df3-414e-b059-551f7c83f43f/dqc_reference/reference_markers_gtdb.fasta -out GCF_023634845.1_ASM2363484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:05,923] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:05,930] [INFO] Selected 22 target genomes.
[2024-01-25 17:52:05,931] [INFO] Target genome list was writen to GCF_023634845.1_ASM2363484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:05,951] [INFO] Task started: fastANI
[2024-01-25 17:52:05,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a8fe3a-21f3-4989-89b1-ab6f85b554c9/GCF_023634845.1_ASM2363484v1_genomic.fna.gz --refList GCF_023634845.1_ASM2363484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023634845.1_ASM2363484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:20,404] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:20,418] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:52:20,418] [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_004959765.1	s__Flavobacterium sp004959765	79.7016	437	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	79.6241	398	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	78.8164	344	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498475.1	s__Flavobacterium cauense	78.2853	247	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCA_018062725.1	s__Flavobacterium sp018062725	78.2717	224	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002204895.1	s__Flavobacterium columnare_C	78.2586	174	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCF_000430025.1	s__Flavobacterium suncheonense	77.9818	201	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000498495.1	s__Flavobacterium enshiense	77.7939	250	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004801375.1	s__Flavobacterium sp004801375	77.5971	196	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119235.1	s__Flavobacterium phycosphaerae	77.5969	186	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787805.1	s__Flavobacterium sp016787805	77.5044	142	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	77.4914	184	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.4779	114	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151275.1	s__Flavobacterium sp004151275	77.4547	108	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129795.1	s__Flavobacterium sp900129795	77.3663	184	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000016645.1	s__Flavobacterium johnsoniae	77.3555	185	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.23	96.72	0.94	0.86	7	-
GCF_014596575.1	s__Flavobacterium pokkalii	77.2619	172	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.93	96.93	0.85	0.85	2	-
GCF_004122145.1	s__Flavobacterium piscinae	77.2017	146	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCF_003314435.2	s__Flavobacterium petrolei	77.1959	163	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCA_003243255.1	s__Flavobacterium psychrophilum_B	77.1769	110	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000769915.1	s__Flavobacterium beibuense	77.0163	120	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296885.1	s__Flavobacterium sp002296885	76.9791	120	1404	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:20,423] [INFO] GTDB search result was written to GCF_023634845.1_ASM2363484v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:20,423] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:20,428] [INFO] DFAST_QC result json was written to GCF_023634845.1_ASM2363484v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:20,428] [INFO] DFAST_QC completed!
[2024-01-25 17:52:20,428] [INFO] Total running time: 0h1m30s