[2024-01-24 12:22:14,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:14,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:14,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference
[2024-01-24 12:22:15,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:15,735] [INFO] Task started: Prodigal
[2024-01-24 12:22:15,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg30eb1b1e-8681-4e71-9472-ce8f883b2844/GCF_020886115.1_ASM2088611v1_genomic.fna.gz | prodigal -d GCF_020886115.1_ASM2088611v1_genomic.fna/cds.fna -a GCF_020886115.1_ASM2088611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:25,485] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:25,485] [INFO] Task started: HMMsearch
[2024-01-24 12:22:25,485] [INFO] Running command: hmmsearch --tblout GCF_020886115.1_ASM2088611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/reference_markers.hmm GCF_020886115.1_ASM2088611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:25,808] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:25,809] [INFO] Found 6/6 markers.
[2024-01-24 12:22:25,839] [INFO] Query marker FASTA was written to GCF_020886115.1_ASM2088611v1_genomic.fna/markers.fasta
[2024-01-24 12:22:25,840] [INFO] Task started: Blastn
[2024-01-24 12:22:25,840] [INFO] Running command: blastn -query GCF_020886115.1_ASM2088611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/reference_markers.fasta -out GCF_020886115.1_ASM2088611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:26,639] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:26,645] [INFO] Selected 32 target genomes.
[2024-01-24 12:22:26,645] [INFO] Target genome list was writen to GCF_020886115.1_ASM2088611v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:26,666] [INFO] Task started: fastANI
[2024-01-24 12:22:26,666] [INFO] Running command: fastANI --query /var/lib/cwl/stg30eb1b1e-8681-4e71-9472-ce8f883b2844/GCF_020886115.1_ASM2088611v1_genomic.fna.gz --refList GCF_020886115.1_ASM2088611v1_genomic.fna/target_genomes.txt --output GCF_020886115.1_ASM2088611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:47,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:47,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:47,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:47,927] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:47,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:47,928] [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 gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.1697	342	803	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	79.1073	188	803	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	79.0777	343	803	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	78.9605	336	803	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	78.9397	349	803	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_001686935.1	551990	551990	type	True	78.8695	274	803	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	78.8663	332	803	95	below_threshold
Flavobacterium daemonense	strain=JCM 19455	GCA_007341385.1	1393049	1393049	type	True	78.8655	269	803	95	below_threshold
Flavobacterium glycines	strain=NBRC 105008	GCA_007989005.1	551990	551990	type	True	78.8212	278	803	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	78.7882	338	803	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	78.7828	337	803	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	78.7798	345	803	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	78.7224	315	803	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.7201	272	803	95	below_threshold
Flavobacterium glycines	strain=Gm-149	GCA_900100165.1	551990	551990	type	True	78.7184	276	803	95	below_threshold
Flavobacterium caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	78.6904	317	803	95	below_threshold
Flavobacterium reichenbachii	strain=DSM 21791	GCA_002217435.1	362418	362418	type	True	78.6864	274	803	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	78.6563	337	803	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	78.6553	297	803	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.6519	306	803	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	78.6353	277	803	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	78.631	311	803	95	below_threshold
Flavobacterium micromati	strain=DSM 17659	GCA_900129585.1	229205	229205	type	True	78.5639	283	803	95	below_threshold
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	78.5107	315	803	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	78.4969	290	803	95	below_threshold
Flavobacterium pectinovorum	strain=ATCC 19366	GCA_002217365.1	29533	29533	type	True	78.4961	294	803	95	below_threshold
Flavobacterium pectinovorum	strain=DSM 6368	GCA_900142715.1	29533	29533	type	True	78.4846	288	803	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.2794	211	803	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.2093	200	803	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.906	219	803	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.7886	163	803	95	below_threshold
Flavobacterium tegetincola	strain=DSM 22377	GCA_000425485.1	150172	150172	type	True	77.7274	189	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,931] [INFO] DFAST Taxonomy check result was written to GCF_020886115.1_ASM2088611v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:47,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:47,932] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:47,932] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/checkm_data
[2024-01-24 12:22:47,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:47,964] [INFO] Task started: CheckM
[2024-01-24 12:22:47,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020886115.1_ASM2088611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020886115.1_ASM2088611v1_genomic.fna/checkm_input GCF_020886115.1_ASM2088611v1_genomic.fna/checkm_result
[2024-01-24 12:23:22,458] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:22,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:22,477] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:22,477] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:22,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020886115.1_ASM2088611v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:22,478] [INFO] Task started: Blastn
[2024-01-24 12:23:22,478] [INFO] Running command: blastn -query GCF_020886115.1_ASM2088611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ac32018-1960-4965-9ab0-252586b6df4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_020886115.1_ASM2088611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:23,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:23,508] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:23,508] [INFO] Target genome list was writen to GCF_020886115.1_ASM2088611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:23,521] [INFO] Task started: fastANI
[2024-01-24 12:23:23,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg30eb1b1e-8681-4e71-9472-ce8f883b2844/GCF_020886115.1_ASM2088611v1_genomic.fna.gz --refList GCF_020886115.1_ASM2088611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020886115.1_ASM2088611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:32,826] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:32,840] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:23:32,840] [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_017988155.1	s__Flavobacterium sp017988155	89.132	373	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984035.1	s__Flavobacterium sp017984035	84.4963	360	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001800905.1	s__Flavobacterium sp001800905	84.4919	567	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002382495.1	s__Flavobacterium sp002382495	84.3127	483	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634825.1	s__Flavobacterium sp003634825	79.9104	399	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	78.9605	336	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351595.1	s__Flavobacterium sp015351595	78.8389	310	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984835.1	s__Flavobacterium sp017984835	78.7005	192	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.46	99.46	0.94	0.94	2	-
GCF_001428525.1	s__Flavobacterium sp001428525	78.6706	269	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	78.6532	305	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_004349135.1	s__Flavobacterium sandaracinum	78.6443	338	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142735.1	s__Flavobacterium saccharophilum	78.6415	298	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217415.1	s__Flavobacterium sp003217415	78.6232	303	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.56	98.67	0.98	0.94	4	-
GCF_000282055.1	s__Flavobacterium sp000282055	78.4062	287	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	77.9237	211	803	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:32,844] [INFO] GTDB search result was written to GCF_020886115.1_ASM2088611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:32,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:32,857] [INFO] DFAST_QC result json was written to GCF_020886115.1_ASM2088611v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:32,858] [INFO] DFAST_QC completed!
[2024-01-24 12:23:32,858] [INFO] Total running time: 0h1m19s