[2024-01-25 20:14:50,996] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,997] [INFO] DQC Reference Directory: /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference
[2024-01-25 20:14:52,123] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:52,124] [INFO] Task started: Prodigal
[2024-01-25 20:14:52,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ea615c4-9176-4dbb-a720-60e028fd6675/GCF_014651275.1_ASM1465127v1_genomic.fna.gz | prodigal -d GCF_014651275.1_ASM1465127v1_genomic.fna/cds.fna -a GCF_014651275.1_ASM1465127v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:03,609] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:03,609] [INFO] Task started: HMMsearch
[2024-01-25 20:15:03,609] [INFO] Running command: hmmsearch --tblout GCF_014651275.1_ASM1465127v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/reference_markers.hmm GCF_014651275.1_ASM1465127v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:03,853] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:03,854] [INFO] Found 6/6 markers.
[2024-01-25 20:15:03,885] [INFO] Query marker FASTA was written to GCF_014651275.1_ASM1465127v1_genomic.fna/markers.fasta
[2024-01-25 20:15:03,885] [INFO] Task started: Blastn
[2024-01-25 20:15:03,886] [INFO] Running command: blastn -query GCF_014651275.1_ASM1465127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/reference_markers.fasta -out GCF_014651275.1_ASM1465127v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:04,519] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:04,522] [INFO] Selected 23 target genomes.
[2024-01-25 20:15:04,523] [INFO] Target genome list was writen to GCF_014651275.1_ASM1465127v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:04,529] [INFO] Task started: fastANI
[2024-01-25 20:15:04,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea615c4-9176-4dbb-a720-60e028fd6675/GCF_014651275.1_ASM1465127v1_genomic.fna.gz --refList GCF_014651275.1_ASM1465127v1_genomic.fna/target_genomes.txt --output GCF_014651275.1_ASM1465127v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:18,392] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:18,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:18,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:18,406] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:15:18,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:18,406] [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
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	100.0	1238	1238	95	conclusive
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	99.9729	1233	1238	95	conclusive
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	78.1307	357	1238	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7504	134	1238	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.5763	249	1238	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.514	140	1238	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	77.4056	221	1238	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	77.3294	185	1238	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	77.2442	175	1238	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.2243	230	1238	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	77.1857	194	1238	95	below_threshold
Formosa agariphila	strain=type strain: KMM 3901	GCA_000723205.1	320324	320324	type	True	77.1541	132	1238	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.1433	113	1238	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.1368	104	1238	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.1311	153	1238	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	77.1158	142	1238	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	77.0463	141	1238	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.9522	134	1238	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9487	77	1238	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.8251	50	1238	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	76.8133	89	1238	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.7459	84	1238	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.6613	99	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:18,408] [INFO] DFAST Taxonomy check result was written to GCF_014651275.1_ASM1465127v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:18,411] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:18,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:18,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/checkm_data
[2024-01-25 20:15:18,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:18,452] [INFO] Task started: CheckM
[2024-01-25 20:15:18,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651275.1_ASM1465127v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651275.1_ASM1465127v1_genomic.fna/checkm_input GCF_014651275.1_ASM1465127v1_genomic.fna/checkm_result
[2024-01-25 20:15:54,768] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:54,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:54,788] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:54,788] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:54,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651275.1_ASM1465127v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:54,789] [INFO] Task started: Blastn
[2024-01-25 20:15:54,789] [INFO] Running command: blastn -query GCF_014651275.1_ASM1465127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec90cf15-f587-4a40-a974-e540c0b2e7d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651275.1_ASM1465127v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:55,741] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:55,745] [INFO] Selected 21 target genomes.
[2024-01-25 20:15:55,745] [INFO] Target genome list was writen to GCF_014651275.1_ASM1465127v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:55,801] [INFO] Task started: fastANI
[2024-01-25 20:15:55,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ea615c4-9176-4dbb-a720-60e028fd6675/GCF_014651275.1_ASM1465127v1_genomic.fna.gz --refList GCF_014651275.1_ASM1465127v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651275.1_ASM1465127v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:08,932] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:08,957] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:08,958] [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_900102055.1	s__Ulvibacter litoralis	99.9729	1233	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003688405.1	s__Ulvibacter antarcticus	78.1833	355	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	77.836	214	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.579	248	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009014635.1	s__Patiriisocius marinistellae	77.4228	197	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	77.4056	221	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	77.3924	222	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002364245.1	s__Marixanthomonas sp002364245	77.3295	153	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	77.3136	186	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_000723205.1	s__Formosa agariphila	77.2666	133	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.2365	229	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	77.2095	195	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	77.1857	194	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	77.1681	112	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCA_011044175.1	s__Marinirhabdus sp011044175	77.1604	202	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106795.1	s__Aequorivita viscosa	77.1158	142	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.0851	114	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	77.0372	190	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.9893	172	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	76.9522	134	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016827605.1	s__Jejuia sp016827605	76.8868	79	1238	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:08,959] [INFO] GTDB search result was written to GCF_014651275.1_ASM1465127v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:08,960] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:08,964] [INFO] DFAST_QC result json was written to GCF_014651275.1_ASM1465127v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:08,964] [INFO] DFAST_QC completed!
[2024-01-25 20:16:08,965] [INFO] Total running time: 0h1m18s