[2024-01-24 13:40:55,500] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,511] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference
[2024-01-24 13:40:56,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,860] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,861] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1062eaa-c662-4963-b230-831adcbf6ba5/GCF_003148385.1_ASM314838v1_genomic.fna.gz | prodigal -d GCF_003148385.1_ASM314838v1_genomic.fna/cds.fna -a GCF_003148385.1_ASM314838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:08,971] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:08,971] [INFO] Task started: HMMsearch
[2024-01-24 13:41:08,971] [INFO] Running command: hmmsearch --tblout GCF_003148385.1_ASM314838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/reference_markers.hmm GCF_003148385.1_ASM314838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:09,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:09,284] [INFO] Found 6/6 markers.
[2024-01-24 13:41:09,319] [INFO] Query marker FASTA was written to GCF_003148385.1_ASM314838v1_genomic.fna/markers.fasta
[2024-01-24 13:41:09,320] [INFO] Task started: Blastn
[2024-01-24 13:41:09,320] [INFO] Running command: blastn -query GCF_003148385.1_ASM314838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/reference_markers.fasta -out GCF_003148385.1_ASM314838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:10,096] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:10,099] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:10,100] [INFO] Target genome list was writen to GCF_003148385.1_ASM314838v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:10,104] [INFO] Task started: fastANI
[2024-01-24 13:41:10,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1062eaa-c662-4963-b230-831adcbf6ba5/GCF_003148385.1_ASM314838v1_genomic.fna.gz --refList GCF_003148385.1_ASM314838v1_genomic.fna/target_genomes.txt --output GCF_003148385.1_ASM314838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:21,050] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:21,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:21,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:21,070] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:21,070] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:21,070] [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 sediminis	strain=MEBiC07310	GCA_003148385.1	2201181	2201181	type	True	100.0	1146	1147	95	conclusive
Flavobacterium haoranii	strain=KCTC 23008	GCA_009363055.1	683124	683124	type	True	79.7713	388	1147	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	79.6096	384	1147	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.335	262	1147	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.27	260	1147	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.2379	297	1147	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.2379	297	1147	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	78.1317	152	1147	95	below_threshold
Flavobacterium indicum	strain=GPTSA100-9	GCA_000455605.1	312277	312277	type	True	78.0679	193	1147	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.0057	225	1147	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.9708	267	1147	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	77.9516	251	1147	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	77.9212	279	1147	95	below_threshold
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	77.9154	253	1147	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.697	247	1147	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	77.2435	133	1147	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.1088	144	1147	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.0275	133	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,072] [INFO] DFAST Taxonomy check result was written to GCF_003148385.1_ASM314838v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:21,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:21,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:21,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/checkm_data
[2024-01-24 13:41:21,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:21,116] [INFO] Task started: CheckM
[2024-01-24 13:41:21,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003148385.1_ASM314838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003148385.1_ASM314838v1_genomic.fna/checkm_input GCF_003148385.1_ASM314838v1_genomic.fna/checkm_result
[2024-01-24 13:42:02,202] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:02,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,228] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:02,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:02,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003148385.1_ASM314838v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:02,229] [INFO] Task started: Blastn
[2024-01-24 13:42:02,229] [INFO] Running command: blastn -query GCF_003148385.1_ASM314838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4830e9c-4555-48f4-b9c5-77eeb2d9f51a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003148385.1_ASM314838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:03,159] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:03,163] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:03,163] [INFO] Target genome list was writen to GCF_003148385.1_ASM314838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:03,173] [INFO] Task started: fastANI
[2024-01-24 13:42:03,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1062eaa-c662-4963-b230-831adcbf6ba5/GCF_003148385.1_ASM314838v1_genomic.fna.gz --refList GCF_003148385.1_ASM314838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003148385.1_ASM314838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:12,908] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:12,923] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:12,923] [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_003148385.1	s__Flavobacterium sediminis	100.0	1146	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003246205.1	s__Flavobacterium haoranii_A	86.5718	659	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363055.1	s__Flavobacterium haoranii	79.7835	386	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002715085.1	s__Flavobacterium sp002715085	78.9155	263	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763515.1	s__Flavobacterium sp014763515	78.5937	202	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	78.3808	258	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.2379	297	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000455605.1	s__Flavobacterium indicum	78.1485	192	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	78.071	271	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.0057	225	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003293845.1	s__Flavobacterium tibetense	77.9684	251	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	77.939	258	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	77.9154	253	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422095.1	s__Flavobacterium sp002422095	77.8482	212	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862755.1	s__Flavobacterium sp002862755	77.7706	262	1147	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	77.5803	147	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCA_012032075.1	s__Flavobacterium sp012032075	77.3289	195	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	77.1539	159	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,925] [INFO] GTDB search result was written to GCF_003148385.1_ASM314838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:12,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:12,929] [INFO] DFAST_QC result json was written to GCF_003148385.1_ASM314838v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:12,929] [INFO] DFAST_QC completed!
[2024-01-24 13:42:12,929] [INFO] Total running time: 0h1m17s