[2024-01-24 14:05:53,907] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,909] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,909] [INFO] DQC Reference Directory: /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference
[2024-01-24 14:05:55,317] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,318] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,318] [INFO] Running command: gunzip -c /var/lib/cwl/stgee05abd9-47d1-4b84-987a-e5a8a7cc21cd/GCF_003076455.1_ASM307645v1_genomic.fna.gz | prodigal -d GCF_003076455.1_ASM307645v1_genomic.fna/cds.fna -a GCF_003076455.1_ASM307645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:15,093] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:15,094] [INFO] Task started: HMMsearch
[2024-01-24 14:06:15,094] [INFO] Running command: hmmsearch --tblout GCF_003076455.1_ASM307645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/reference_markers.hmm GCF_003076455.1_ASM307645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:15,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:15,434] [INFO] Found 6/6 markers.
[2024-01-24 14:06:15,473] [INFO] Query marker FASTA was written to GCF_003076455.1_ASM307645v1_genomic.fna/markers.fasta
[2024-01-24 14:06:15,473] [INFO] Task started: Blastn
[2024-01-24 14:06:15,473] [INFO] Running command: blastn -query GCF_003076455.1_ASM307645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/reference_markers.fasta -out GCF_003076455.1_ASM307645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:16,231] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:16,235] [INFO] Selected 26 target genomes.
[2024-01-24 14:06:16,236] [INFO] Target genome list was writen to GCF_003076455.1_ASM307645v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:16,249] [INFO] Task started: fastANI
[2024-01-24 14:06:16,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgee05abd9-47d1-4b84-987a-e5a8a7cc21cd/GCF_003076455.1_ASM307645v1_genomic.fna.gz --refList GCF_003076455.1_ASM307645v1_genomic.fna/target_genomes.txt --output GCF_003076455.1_ASM307645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:35,142] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:35,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:35,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:35,164] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:35,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:35,164] [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 faecale	strain=WV33	GCA_003076455.1	1355330	1355330	type	True	100.0	1538	1540	95	conclusive
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	79.688	399	1540	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	79.6077	369	1540	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	79.5208	412	1540	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	79.4681	428	1540	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	79.2853	360	1540	95	below_threshold
Flavobacterium kayseriense	strain=F-47	GCA_014305095.1	2764714	2764714	type	True	79.1311	355	1540	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	79.0533	346	1540	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	79.0175	295	1540	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	78.9567	334	1540	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	78.9553	331	1540	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	78.9275	329	1540	95	below_threshold
Flavobacterium palustre	strain=CGMCC 1.12811	GCA_014639535.1	1476463	1476463	type	True	78.9216	313	1540	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	78.8398	311	1540	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	78.7394	347	1540	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	78.7154	338	1540	95	below_threshold
Flavobacterium omnivorum	strain=CGMCC 1.2747	GCA_900099915.1	178355	178355	type	True	78.6755	310	1540	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	78.5927	344	1540	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.5793	307	1540	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	78.5578	299	1540	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.5269	290	1540	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	78.4373	305	1540	95	below_threshold
Flavobacterium tiangeerense	strain=CGMCC 1.6847	GCA_007830355.1	459471	459471	type	True	78.3165	302	1540	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.9915	164	1540	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.9251	172	1540	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.9088	184	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:35,166] [INFO] DFAST Taxonomy check result was written to GCF_003076455.1_ASM307645v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:35,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:35,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:35,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/checkm_data
[2024-01-24 14:06:35,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:35,218] [INFO] Task started: CheckM
[2024-01-24 14:06:35,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003076455.1_ASM307645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003076455.1_ASM307645v1_genomic.fna/checkm_input GCF_003076455.1_ASM307645v1_genomic.fna/checkm_result
[2024-01-24 14:07:30,399] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:30,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:30,423] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:30,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:30,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003076455.1_ASM307645v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:30,425] [INFO] Task started: Blastn
[2024-01-24 14:07:30,425] [INFO] Running command: blastn -query GCF_003076455.1_ASM307645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6b58a57-1fc7-49a2-bc1d-566883673d16/dqc_reference/reference_markers_gtdb.fasta -out GCF_003076455.1_ASM307645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:31,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:31,349] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:31,349] [INFO] Target genome list was writen to GCF_003076455.1_ASM307645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:31,364] [INFO] Task started: fastANI
[2024-01-24 14:07:31,364] [INFO] Running command: fastANI --query /var/lib/cwl/stgee05abd9-47d1-4b84-987a-e5a8a7cc21cd/GCF_003076455.1_ASM307645v1_genomic.fna.gz --refList GCF_003076455.1_ASM307645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003076455.1_ASM307645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:48,948] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:48,971] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:48,971] [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_003076455.1	s__Flavobacterium faecale	100.0	1538	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013294005.1	s__Flavobacterium sp013294005	80.5948	496	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.41	97.36	0.86	0.85	3	-
GCF_013294025.1	s__Flavobacterium sp013294025	80.446	444	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425505.1	s__Flavobacterium frigidarium	79.6892	398	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305155.1	s__Flavobacterium sp014305155	79.4685	428	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002813295.1	s__Flavobacterium sp002813295	79.2968	330	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	79.2963	360	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014305095.1	s__Flavobacterium kayseriense	79.1446	354	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.16	98.32	0.96	0.92	3	-
GCF_004016525.1	s__Flavobacterium sufflavum	79.0394	348	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688495.1	s__Flavobacterium weaverense	79.0114	296	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284035.1	s__Flavobacterium sp003096795	78.9694	313	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.66	97.66	0.93	0.93	2	-
GCF_000695795.1	s__Flavobacterium seoulense	78.9648	334	1540	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	78.9443	346	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
GCF_014639535.1	s__Flavobacterium palustre	78.9131	316	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280815.1	s__Flavobacterium sp002280815	78.8517	311	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	78.7162	338	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754195.1	s__Flavobacterium sp002754195	78.6969	349	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339525.1	s__Flavobacterium sp004339525	78.5884	341	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015752255.1	s__Flavobacterium sp015752255	78.4874	330	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254565.1	s__Flavobacterium nitrogenifigens	78.3996	273	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001429295.1	s__Flavobacterium sp001429295	78.1121	303	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.90	97.90	0.95	0.95	2	-
GCF_015277675.1	s__Flavobacterium soyangense	77.984	264	1540	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:48,973] [INFO] GTDB search result was written to GCF_003076455.1_ASM307645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:48,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:48,979] [INFO] DFAST_QC result json was written to GCF_003076455.1_ASM307645v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:48,979] [INFO] DFAST_QC completed!
[2024-01-24 14:07:48,980] [INFO] Total running time: 0h1m55s