[2024-01-24 14:31:14,405] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,408] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference
[2024-01-24 14:31:15,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,786] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,786] [INFO] Running command: gunzip -c /var/lib/cwl/stga200a1d0-cae2-4818-9463-cf67a4445a62/GCF_009014635.1_ASM901463v1_genomic.fna.gz | prodigal -d GCF_009014635.1_ASM901463v1_genomic.fna/cds.fna -a GCF_009014635.1_ASM901463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:27,487] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:27,487] [INFO] Task started: HMMsearch
[2024-01-24 14:31:27,487] [INFO] Running command: hmmsearch --tblout GCF_009014635.1_ASM901463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/reference_markers.hmm GCF_009014635.1_ASM901463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:27,786] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:27,787] [INFO] Found 6/6 markers.
[2024-01-24 14:31:27,825] [INFO] Query marker FASTA was written to GCF_009014635.1_ASM901463v1_genomic.fna/markers.fasta
[2024-01-24 14:31:27,825] [INFO] Task started: Blastn
[2024-01-24 14:31:27,825] [INFO] Running command: blastn -query GCF_009014635.1_ASM901463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/reference_markers.fasta -out GCF_009014635.1_ASM901463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:28,534] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:28,537] [INFO] Selected 27 target genomes.
[2024-01-24 14:31:28,538] [INFO] Target genome list was writen to GCF_009014635.1_ASM901463v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:28,546] [INFO] Task started: fastANI
[2024-01-24 14:31:28,547] [INFO] Running command: fastANI --query /var/lib/cwl/stga200a1d0-cae2-4818-9463-cf67a4445a62/GCF_009014635.1_ASM901463v1_genomic.fna.gz --refList GCF_009014635.1_ASM901463v1_genomic.fna/target_genomes.txt --output GCF_009014635.1_ASM901463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:47,098] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:47,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:47,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:47,123] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:47,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:47,124] [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
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	100.0	1099	1100	95	conclusive
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	78.0468	383	1100	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	77.6189	139	1100	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.3312	209	1100	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.2556	210	1100	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.2142	103	1100	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	77.0673	121	1100	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.0294	155	1100	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.0281	125	1100	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.0079	126	1100	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9306	98	1100	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	76.9029	110	1100	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.8979	197	1100	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.8935	136	1100	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.8501	140	1100	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.7457	138	1100	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7315	64	1100	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.7234	117	1100	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.7213	108	1100	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.4187	105	1100	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	76.4016	114	1100	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.3472	95	1100	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.0968	125	1100	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.0472	62	1100	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.0222	117	1100	95	below_threshold
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	75.8497	87	1100	95	below_threshold
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	75.7902	87	1100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:47,125] [INFO] DFAST Taxonomy check result was written to GCF_009014635.1_ASM901463v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:47,126] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:47,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:47,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/checkm_data
[2024-01-24 14:31:47,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:47,161] [INFO] Task started: CheckM
[2024-01-24 14:31:47,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009014635.1_ASM901463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009014635.1_ASM901463v1_genomic.fna/checkm_input GCF_009014635.1_ASM901463v1_genomic.fna/checkm_result
[2024-01-24 14:32:23,262] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:23,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:23,283] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:23,283] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:23,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009014635.1_ASM901463v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:23,284] [INFO] Task started: Blastn
[2024-01-24 14:32:23,284] [INFO] Running command: blastn -query GCF_009014635.1_ASM901463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15a8f1f2-c004-4f3e-91f8-341d3442a2cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009014635.1_ASM901463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:24,230] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:24,234] [INFO] Selected 22 target genomes.
[2024-01-24 14:32:24,235] [INFO] Target genome list was writen to GCF_009014635.1_ASM901463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:24,252] [INFO] Task started: fastANI
[2024-01-24 14:32:24,252] [INFO] Running command: fastANI --query /var/lib/cwl/stga200a1d0-cae2-4818-9463-cf67a4445a62/GCF_009014635.1_ASM901463v1_genomic.fna.gz --refList GCF_009014635.1_ASM901463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009014635.1_ASM901463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:39,375] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:39,394] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:39,394] [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_009014635.1	s__Patiriisocius marinistellae	100.0	1099	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008974325.1	s__Patiriisocius marinus	78.0402	383	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182755.1	s__Patiriisocius sp905182755	77.9342	155	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	96.66	96.28	0.84	0.84	6	-
GCA_003450155.1	s__Patiriisocius sp003450155	77.7781	164	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000170815.1	s__Patiriisocius sp000170815	77.3882	282	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.2556	210	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.1311	146	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707745.1	s__Marinirhabdus sp002707745	76.9853	106	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCA_002713705.1	s__GCA-002733185 sp002713705	76.9847	101	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.9583	125	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_900099995.1	s__Winogradskyella thalassocola	76.8758	137	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.7636	133	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	76.7149	127	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_002895005.1	s__Hanstruepera neustonica	76.6958	65	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003443635.1	s__AU392 sp003443635	76.6898	113	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__AU392	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.6738	163	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694465.1	s__IN17 sp002694465	76.5704	127	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.93	99.93	0.95	0.95	2	-
GCF_015319355.1	s__Psychroserpens luteus	76.5334	167	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.4534	110	1100	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_011762485.1	s__Yeosuana marina	76.4187	105	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.2568	100	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	76.0996	126	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:39,396] [INFO] GTDB search result was written to GCF_009014635.1_ASM901463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:39,397] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:39,403] [INFO] DFAST_QC result json was written to GCF_009014635.1_ASM901463v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:39,403] [INFO] DFAST_QC completed!
[2024-01-24 14:32:39,403] [INFO] Total running time: 0h1m25s