[2024-01-24 13:13:12,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference
[2024-01-24 13:13:13,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,901] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,902] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe52c597-9859-4f03-b501-bf252b68eadc/GCF_006148925.1_ASM614892v1_genomic.fna.gz | prodigal -d GCF_006148925.1_ASM614892v1_genomic.fna/cds.fna -a GCF_006148925.1_ASM614892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:24,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:24,004] [INFO] Task started: HMMsearch
[2024-01-24 13:13:24,004] [INFO] Running command: hmmsearch --tblout GCF_006148925.1_ASM614892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/reference_markers.hmm GCF_006148925.1_ASM614892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:24,281] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:24,282] [INFO] Found 6/6 markers.
[2024-01-24 13:13:24,314] [INFO] Query marker FASTA was written to GCF_006148925.1_ASM614892v1_genomic.fna/markers.fasta
[2024-01-24 13:13:24,314] [INFO] Task started: Blastn
[2024-01-24 13:13:24,314] [INFO] Running command: blastn -query GCF_006148925.1_ASM614892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/reference_markers.fasta -out GCF_006148925.1_ASM614892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:24,991] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:24,995] [INFO] Selected 26 target genomes.
[2024-01-24 13:13:24,995] [INFO] Target genome list was writen to GCF_006148925.1_ASM614892v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:26,002] [INFO] Task started: fastANI
[2024-01-24 13:13:26,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe52c597-9859-4f03-b501-bf252b68eadc/GCF_006148925.1_ASM614892v1_genomic.fna.gz --refList GCF_006148925.1_ASM614892v1_genomic.fna/target_genomes.txt --output GCF_006148925.1_ASM614892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:43,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:43,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:43,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:43,684] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:43,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:43,684] [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
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	100.0	1044	1045	95	conclusive
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.8306	433	1045	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.7934	375	1045	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.7142	378	1045	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.7005	382	1045	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.6393	355	1045	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.6346	356	1045	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.6346	356	1045	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.5653	378	1045	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.383	342	1045	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.2837	337	1045	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.1318	277	1045	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	78.1035	320	1045	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.9354	300	1045	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.9152	215	1045	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.863	224	1045	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.747	228	1045	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.7013	311	1045	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	77.6313	215	1045	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	77.448	211	1045	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.3925	187	1045	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.2818	165	1045	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.2398	215	1045	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.2398	215	1045	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	77.1751	164	1045	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.1489	194	1045	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:43,689] [INFO] DFAST Taxonomy check result was written to GCF_006148925.1_ASM614892v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:43,690] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:43,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:43,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/checkm_data
[2024-01-24 13:13:43,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:43,729] [INFO] Task started: CheckM
[2024-01-24 13:13:43,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006148925.1_ASM614892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006148925.1_ASM614892v1_genomic.fna/checkm_input GCF_006148925.1_ASM614892v1_genomic.fna/checkm_result
[2024-01-24 13:14:18,677] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:18,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,693] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:18,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:18,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006148925.1_ASM614892v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:18,694] [INFO] Task started: Blastn
[2024-01-24 13:14:18,694] [INFO] Running command: blastn -query GCF_006148925.1_ASM614892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf906cbd1-3ca3-42fb-9c87-309f0993640d/dqc_reference/reference_markers_gtdb.fasta -out GCF_006148925.1_ASM614892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:19,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:19,635] [INFO] Selected 18 target genomes.
[2024-01-24 13:14:19,636] [INFO] Target genome list was writen to GCF_006148925.1_ASM614892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:19,662] [INFO] Task started: fastANI
[2024-01-24 13:14:19,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe52c597-9859-4f03-b501-bf252b68eadc/GCF_006148925.1_ASM614892v1_genomic.fna.gz --refList GCF_006148925.1_ASM614892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006148925.1_ASM614892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:32,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:32,749] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:32,750] [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_006148925.1	s__Algibacter_D aestuarii	100.0	1044	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003143755.1	s__Algibacter_B sp003143755	78.8299	433	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.8044	374	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.703	359	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.696	383	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114265.1	s__Flaviramulus basaltis	78.6889	427	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.6545	409	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.6393	355	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002741945.1	s__Wocania sp002741945	78.5701	399	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.5658	379	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	78.3817	326	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	78.3787	343	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.3227	329	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.5745	235	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.3316	219	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	77.2398	215	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900099995.1	s__Winogradskyella thalassocola	77.1489	194	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	76.6981	177	1045	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:32,752] [INFO] GTDB search result was written to GCF_006148925.1_ASM614892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:32,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:32,758] [INFO] DFAST_QC result json was written to GCF_006148925.1_ASM614892v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:32,758] [INFO] DFAST_QC completed!
[2024-01-24 13:14:32,759] [INFO] Total running time: 0h1m20s