[2024-01-25 18:39:35,534] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference
[2024-01-25 18:39:36,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,681] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg28e51103-e80c-40fc-97a7-13f63b473182/GCF_000429545.1_ASM42954v1_genomic.fna.gz | prodigal -d GCF_000429545.1_ASM42954v1_genomic.fna/cds.fna -a GCF_000429545.1_ASM42954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:52,312] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:52,312] [INFO] Task started: HMMsearch
[2024-01-25 18:39:52,312] [INFO] Running command: hmmsearch --tblout GCF_000429545.1_ASM42954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/reference_markers.hmm GCF_000429545.1_ASM42954v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:52,609] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:52,610] [INFO] Found 6/6 markers.
[2024-01-25 18:39:52,651] [INFO] Query marker FASTA was written to GCF_000429545.1_ASM42954v1_genomic.fna/markers.fasta
[2024-01-25 18:39:52,651] [INFO] Task started: Blastn
[2024-01-25 18:39:52,652] [INFO] Running command: blastn -query GCF_000429545.1_ASM42954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/reference_markers.fasta -out GCF_000429545.1_ASM42954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:53,280] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:53,283] [INFO] Selected 16 target genomes.
[2024-01-25 18:39:53,284] [INFO] Target genome list was writen to GCF_000429545.1_ASM42954v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:53,291] [INFO] Task started: fastANI
[2024-01-25 18:39:53,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e51103-e80c-40fc-97a7-13f63b473182/GCF_000429545.1_ASM42954v1_genomic.fna.gz --refList GCF_000429545.1_ASM42954v1_genomic.fna/target_genomes.txt --output GCF_000429545.1_ASM42954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:07,844] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:07,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:07,846] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:07,855] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:40:07,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:07,856] [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
Arenibacter certesii	strain=DSM 19833	GCA_000429545.1	228955	228955	type	True	100.0	1619	1622	95	conclusive
Arenibacter certesii	strain=KCTC 12113	GCA_014651295.1	228955	228955	type	True	99.9797	1582	1622	95	conclusive
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	85.6404	1169	1622	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	77.9352	363	1622	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	77.924	334	1622	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	77.8759	313	1622	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	77.8498	315	1622	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	77.844	297	1622	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	77.7923	314	1622	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	77.5953	345	1622	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.5021	125	1622	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.3414	129	1622	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.0423	52	1622	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.0242	58	1622	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:07,858] [INFO] DFAST Taxonomy check result was written to GCF_000429545.1_ASM42954v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:07,859] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:07,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:07,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/checkm_data
[2024-01-25 18:40:07,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:07,921] [INFO] Task started: CheckM
[2024-01-25 18:40:07,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429545.1_ASM42954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429545.1_ASM42954v1_genomic.fna/checkm_input GCF_000429545.1_ASM42954v1_genomic.fna/checkm_result
[2024-01-25 18:40:51,957] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:51,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:51,977] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:51,978] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:51,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429545.1_ASM42954v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:51,978] [INFO] Task started: Blastn
[2024-01-25 18:40:51,978] [INFO] Running command: blastn -query GCF_000429545.1_ASM42954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaa5fc93-9945-4a6a-bd6a-a16855d76f8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429545.1_ASM42954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:52,922] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:52,925] [INFO] Selected 18 target genomes.
[2024-01-25 18:40:52,925] [INFO] Target genome list was writen to GCF_000429545.1_ASM42954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:52,934] [INFO] Task started: fastANI
[2024-01-25 18:40:52,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e51103-e80c-40fc-97a7-13f63b473182/GCF_000429545.1_ASM42954v1_genomic.fna.gz --refList GCF_000429545.1_ASM42954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429545.1_ASM42954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:08,868] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:08,879] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:08,879] [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_000429545.1	s__Arenibacter certesii	100.0	1619	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000424985.1	s__Arenibacter latericius	85.6309	1170	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150785.1	s__Arenibacter amylolyticus	79.6517	665	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.19	99.19	0.91	0.91	2	-
GCF_002909255.1	s__Arenibacter hampyeongensis	77.924	334	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	77.915	330	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	77.8737	313	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_003259375.1	s__Arenibacter echinorum	77.853	314	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957295.1	s__Arenibacter aquaticus	77.844	297	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177645.1	s__Arenibacter troitsensis	77.7923	314	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	77.7868	320	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014397245.1	s__Arenibacter arenosicollis	77.5926	345	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	77.5595	335	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.9519	122	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	76.3414	129	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_013391805.1	s__Galbibacter_A sp013391805	76.1303	62	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883545.1	s__Confluentibacter sp018883545	76.0176	58	1622	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:08,882] [INFO] GTDB search result was written to GCF_000429545.1_ASM42954v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:08,883] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:08,887] [INFO] DFAST_QC result json was written to GCF_000429545.1_ASM42954v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:08,888] [INFO] DFAST_QC completed!
[2024-01-25 18:41:08,888] [INFO] Total running time: 0h1m33s