[2024-01-25 20:20:20,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:20,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:20,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference
[2024-01-25 20:20:21,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:21,937] [INFO] Task started: Prodigal
[2024-01-25 20:20:21,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg709fc0d6-8357-4eb3-81f4-510f96bf47d7/GCF_003813905.1_ASM381390v1_genomic.fna.gz | prodigal -d GCF_003813905.1_ASM381390v1_genomic.fna/cds.fna -a GCF_003813905.1_ASM381390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:30,685] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:30,686] [INFO] Task started: HMMsearch
[2024-01-25 20:20:30,686] [INFO] Running command: hmmsearch --tblout GCF_003813905.1_ASM381390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/reference_markers.hmm GCF_003813905.1_ASM381390v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:30,963] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:30,967] [INFO] Found 6/6 markers.
[2024-01-25 20:20:31,002] [INFO] Query marker FASTA was written to GCF_003813905.1_ASM381390v1_genomic.fna/markers.fasta
[2024-01-25 20:20:31,002] [INFO] Task started: Blastn
[2024-01-25 20:20:31,002] [INFO] Running command: blastn -query GCF_003813905.1_ASM381390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/reference_markers.fasta -out GCF_003813905.1_ASM381390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:31,667] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:31,670] [INFO] Selected 15 target genomes.
[2024-01-25 20:20:31,671] [INFO] Target genome list was writen to GCF_003813905.1_ASM381390v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:31,680] [INFO] Task started: fastANI
[2024-01-25 20:20:31,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg709fc0d6-8357-4eb3-81f4-510f96bf47d7/GCF_003813905.1_ASM381390v1_genomic.fna.gz --refList GCF_003813905.1_ASM381390v1_genomic.fna/target_genomes.txt --output GCF_003813905.1_ASM381390v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:41,792] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:41,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:41,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:41,802] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:41,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:41,803] [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
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	100.0	1179	1180	95	conclusive
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	80.0034	711	1180	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	79.9512	723	1180	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	79.9495	746	1180	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	77.0886	207	1180	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.0098	119	1180	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.9652	118	1180	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.801	207	1180	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.6373	145	1180	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5915	155	1180	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	76.5649	116	1180	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.5365	208	1180	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.4326	166	1180	95	below_threshold
Polaribacter tangerinus	strain=WS2-14	GCA_002201235.1	1920034	1920034	type	True	76.2395	136	1180	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	75.7795	109	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:41,807] [INFO] DFAST Taxonomy check result was written to GCF_003813905.1_ASM381390v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:41,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:41,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:41,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/checkm_data
[2024-01-25 20:20:41,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:41,849] [INFO] Task started: CheckM
[2024-01-25 20:20:41,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003813905.1_ASM381390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003813905.1_ASM381390v1_genomic.fna/checkm_input GCF_003813905.1_ASM381390v1_genomic.fna/checkm_result
[2024-01-25 20:21:09,976] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:09,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:09,996] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:09,996] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:09,997] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003813905.1_ASM381390v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:09,997] [INFO] Task started: Blastn
[2024-01-25 20:21:09,997] [INFO] Running command: blastn -query GCF_003813905.1_ASM381390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c1700a2-b957-40e4-a29f-3e2474550513/dqc_reference/reference_markers_gtdb.fasta -out GCF_003813905.1_ASM381390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:11,086] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:11,088] [INFO] Selected 11 target genomes.
[2024-01-25 20:21:11,089] [INFO] Target genome list was writen to GCF_003813905.1_ASM381390v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:11,107] [INFO] Task started: fastANI
[2024-01-25 20:21:11,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg709fc0d6-8357-4eb3-81f4-510f96bf47d7/GCF_003813905.1_ASM381390v1_genomic.fna.gz --refList GCF_003813905.1_ASM381390v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003813905.1_ASM381390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:18,689] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:18,697] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:18,697] [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_003813905.1	s__Aureibaculum marinum	100.0	1179	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003449015.1	s__Aureibaculum sp003449015	79.9995	711	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006065315.1	s__Aureibaculum sp006065315	79.9594	722	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406085.1	s__Aureibaculum sp016406085	79.958	744	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352665.1	s__Aureibaculum sp002352665	77.9067	365	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511845.1	s__Aureibaculum sp003511845	77.6039	256	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	99.43	99.43	0.80	0.80	2	-
GCF_900141715.1	s__Arenitalea lutea	76.9679	121	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003335675.1	s__Winogradskyella sp003335675	76.6249	71	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	76.5649	116	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.5619	166	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002364335.1	s__Winogradskyella sp002364335	76.081	106	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:18,698] [INFO] GTDB search result was written to GCF_003813905.1_ASM381390v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:18,699] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:18,702] [INFO] DFAST_QC result json was written to GCF_003813905.1_ASM381390v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:18,703] [INFO] DFAST_QC completed!
[2024-01-25 20:21:18,703] [INFO] Total running time: 0h0m58s