[2024-01-24 14:05:53,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference
[2024-01-24 14:05:55,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,150] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,150] [INFO] Running command: gunzip -c /var/lib/cwl/stgafe0fd85-0f1a-4efb-872d-6fa67c4e3f5e/GCF_016595465.1_ASM1659546v1_genomic.fna.gz | prodigal -d GCF_016595465.1_ASM1659546v1_genomic.fna/cds.fna -a GCF_016595465.1_ASM1659546v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:36,104] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:36,105] [INFO] Task started: HMMsearch
[2024-01-24 14:06:36,105] [INFO] Running command: hmmsearch --tblout GCF_016595465.1_ASM1659546v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/reference_markers.hmm GCF_016595465.1_ASM1659546v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:36,452] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:36,454] [INFO] Found 6/6 markers.
[2024-01-24 14:06:36,506] [INFO] Query marker FASTA was written to GCF_016595465.1_ASM1659546v1_genomic.fna/markers.fasta
[2024-01-24 14:06:36,507] [INFO] Task started: Blastn
[2024-01-24 14:06:36,507] [INFO] Running command: blastn -query GCF_016595465.1_ASM1659546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/reference_markers.fasta -out GCF_016595465.1_ASM1659546v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:37,149] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:37,154] [INFO] Selected 25 target genomes.
[2024-01-24 14:06:37,154] [INFO] Target genome list was writen to GCF_016595465.1_ASM1659546v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:37,184] [INFO] Task started: fastANI
[2024-01-24 14:06:37,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe0fd85-0f1a-4efb-872d-6fa67c4e3f5e/GCF_016595465.1_ASM1659546v1_genomic.fna.gz --refList GCF_016595465.1_ASM1659546v1_genomic.fna/target_genomes.txt --output GCF_016595465.1_ASM1659546v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:59,743] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:59,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:59,755] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:59,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:59,755] [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
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	100.0	1899	1906	95	conclusive
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	78.0128	343	1906	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	77.3885	266	1906	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	77.188	147	1906	95	below_threshold
Luteolibacter pohnpeiensis	strain=KCTC 22041	GCA_016595435.1	454153	454153	type	True	77.0034	202	1906	95	below_threshold
Haloferula luteola	strain=YC6886	GCA_014201715.1	595692	595692	type	True	76.7557	110	1906	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.733	86	1906	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	76.5251	70	1906	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	76.0355	91	1906	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	75.7922	90	1906	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	75.6715	64	1906	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	75.5738	78	1906	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	75.07	56	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,757] [INFO] DFAST Taxonomy check result was written to GCF_016595465.1_ASM1659546v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:59,758] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:59,758] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:59,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/checkm_data
[2024-01-24 14:06:59,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:59,813] [INFO] Task started: CheckM
[2024-01-24 14:06:59,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595465.1_ASM1659546v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595465.1_ASM1659546v1_genomic.fna/checkm_input GCF_016595465.1_ASM1659546v1_genomic.fna/checkm_result
[2024-01-24 14:08:55,747] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:55,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:55,772] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:55,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:55,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595465.1_ASM1659546v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:55,773] [INFO] Task started: Blastn
[2024-01-24 14:08:55,773] [INFO] Running command: blastn -query GCF_016595465.1_ASM1659546v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a8dbfff-b229-4f5a-9468-a7e4a1aa5bf6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595465.1_ASM1659546v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:56,608] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:56,612] [INFO] Selected 18 target genomes.
[2024-01-24 14:08:56,613] [INFO] Target genome list was writen to GCF_016595465.1_ASM1659546v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:56,667] [INFO] Task started: fastANI
[2024-01-24 14:08:56,668] [INFO] Running command: fastANI --query /var/lib/cwl/stgafe0fd85-0f1a-4efb-872d-6fa67c4e3f5e/GCF_016595465.1_ASM1659546v1_genomic.fna.gz --refList GCF_016595465.1_ASM1659546v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595465.1_ASM1659546v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:12,088] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:12,107] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:12,108] [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_016595465.1	s__Luteolibacter yonseiensis	100.0	1900	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003820635.1	s__Luteolibacter sp003820635	78.7105	342	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018137965.1	s__Luteolibacter sp018137965	78.0318	341	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919975.1	s__Luteolibacter sp903919975	77.9562	277	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.84	0.96	0.96	3	-
GCA_017798145.1	s__Luteolibacter sp017798145	77.8874	297	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906515.1	s__Luteolibacter sp903906515	77.7748	249	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.85	99.81	0.93	0.92	3	-
GCA_903837825.1	s__Luteolibacter sp903837825	77.4413	166	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307065.1	s__Luteolibacter sp002307065	77.3663	211	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903888515.1	s__Luteolibacter sp903888515	77.1244	232	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.90	99.90	0.94	0.94	2	-
GCA_903934285.1	s__Luteolibacter sp903934285	77.0534	209	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.86	99.86	0.92	0.92	3	-
GCA_017301995.1	s__Luteolibacter sp017301995	77.0318	285	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595435.1	s__Luteolibacter pohnpeiensis	76.9913	203	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908495.1	s__Luteolibacter sp903908495	76.9418	271	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903826205.1	s__Luteolibacter sp903826205	76.9074	220	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.67	99.65	0.89	0.88	3	-
GCA_008932935.1	s__Luteolibacter sp008932935	76.6037	97	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827375.1	s__Luteolibacter sp903827375	76.532	159	1906	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	99.41	99.23	0.90	0.81	16	-
GCF_901827205.1	s__Variovorax sp901827205	75.4822	53	1906	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:12,110] [INFO] GTDB search result was written to GCF_016595465.1_ASM1659546v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:12,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:12,114] [INFO] DFAST_QC result json was written to GCF_016595465.1_ASM1659546v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:12,114] [INFO] DFAST_QC completed!
[2024-01-24 14:09:12,114] [INFO] Total running time: 0h3m18s