[2024-01-24 13:09:29,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference
[2024-01-24 13:09:30,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,518] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,519] [INFO] Running command: gunzip -c /var/lib/cwl/stg36602ff1-cd17-40d3-88c2-f84da105e171/GCF_009192765.1_ASM919276v1_genomic.fna.gz | prodigal -d GCF_009192765.1_ASM919276v1_genomic.fna/cds.fna -a GCF_009192765.1_ASM919276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:56,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:56,591] [INFO] Task started: HMMsearch
[2024-01-24 13:09:56,591] [INFO] Running command: hmmsearch --tblout GCF_009192765.1_ASM919276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/reference_markers.hmm GCF_009192765.1_ASM919276v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:57,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:57,033] [INFO] Found 6/6 markers.
[2024-01-24 13:09:57,081] [INFO] Query marker FASTA was written to GCF_009192765.1_ASM919276v1_genomic.fna/markers.fasta
[2024-01-24 13:09:57,081] [INFO] Task started: Blastn
[2024-01-24 13:09:57,081] [INFO] Running command: blastn -query GCF_009192765.1_ASM919276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/reference_markers.fasta -out GCF_009192765.1_ASM919276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:57,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:57,724] [INFO] Selected 24 target genomes.
[2024-01-24 13:09:57,725] [INFO] Target genome list was writen to GCF_009192765.1_ASM919276v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:57,745] [INFO] Task started: fastANI
[2024-01-24 13:09:57,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg36602ff1-cd17-40d3-88c2-f84da105e171/GCF_009192765.1_ASM919276v1_genomic.fna.gz --refList GCF_009192765.1_ASM919276v1_genomic.fna/target_genomes.txt --output GCF_009192765.1_ASM919276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:20,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:20,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:20,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:20,659] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:20,659] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:20,659] [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
Agriterribacter humi	strain=YJ03	GCA_009192765.1	1104781	1104781	type	True	100.0	1877	1879	95	conclusive
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.1716	60	1879	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.0358	61	1879	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.0159	79	1879	95	below_threshold
Niabella soli	strain=JS13-8; DSM 19437	GCA_000243115.3	446683	446683	type	True	76.0102	83	1879	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	75.9963	67	1879	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	75.9086	67	1879	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	75.7472	60	1879	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	75.6754	68	1879	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.6195	111	1879	95	below_threshold
Niastella populi	strain=CCTCC AB 208238	GCA_002078015.1	550983	550983	type	True	75.5999	88	1879	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	75.5844	72	1879	95	below_threshold
Niastella koreensis	strain=DSM 17620	GCA_002077985.1	354356	354356	type	True	75.3065	91	1879	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.277	87	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:20,661] [INFO] DFAST Taxonomy check result was written to GCF_009192765.1_ASM919276v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:20,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:20,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:20,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/checkm_data
[2024-01-24 13:10:20,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:20,717] [INFO] Task started: CheckM
[2024-01-24 13:10:20,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192765.1_ASM919276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192765.1_ASM919276v1_genomic.fna/checkm_input GCF_009192765.1_ASM919276v1_genomic.fna/checkm_result
[2024-01-24 13:11:33,275] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:33,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:33,298] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:33,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:33,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192765.1_ASM919276v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:33,299] [INFO] Task started: Blastn
[2024-01-24 13:11:33,300] [INFO] Running command: blastn -query GCF_009192765.1_ASM919276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a7fbe4-7dd8-4f41-b052-66ddc8015192/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192765.1_ASM919276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:34,331] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:34,335] [INFO] Selected 19 target genomes.
[2024-01-24 13:11:34,335] [INFO] Target genome list was writen to GCF_009192765.1_ASM919276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:34,385] [INFO] Task started: fastANI
[2024-01-24 13:11:34,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg36602ff1-cd17-40d3-88c2-f84da105e171/GCF_009192765.1_ASM919276v1_genomic.fna.gz --refList GCF_009192765.1_ASM919276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192765.1_ASM919276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:49,291] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:49,309] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:49,309] [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_009192765.1	s__Agriterribacter humi	100.0	1877	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003075435.1	s__Agriterribacter sp003075435	77.0047	351	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	97.00	96.97	0.82	0.82	3	-
GCA_001899685.1	s__Agriterribacter sp001899685	76.8643	324	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	99.97	99.97	0.97	0.97	2	-
GCA_018268105.1	s__Agriterribacter sp018268105	76.7002	263	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243115.2	s__Niabella soli	76.1551	82	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185185.1	s__AWTP1-9 sp016185185	76.1393	79	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710935.1	s__Ferruginibacter sp016710935	76.0724	79	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963365.1	s__AWTP1-9 sp003963365	76.0332	88	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140985.1	s__JJ008 sp013140985	75.7464	61	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786785.1	s__Flavitalea sp016786785	75.729	50	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003175935.1	s__Agriterribacter sp003175935	75.697	79	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719015.1	s__JJ008 sp016719015	75.6547	58	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.23	99.17	0.95	0.92	9	-
GCA_016200915.1	s__AWTP1-9 sp016200915	75.6413	102	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
GCF_017356035.1	s__Niastella sp017356035	75.566	81	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336115.1	s__Lacibacter sp002336115	75.4347	66	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	99.94	99.94	0.95	0.95	2	-
GCA_903870685.1	s__CAILAF01 sp903870685	75.3653	52	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.70	99.46	0.92	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:49,311] [INFO] GTDB search result was written to GCF_009192765.1_ASM919276v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:49,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:49,315] [INFO] DFAST_QC result json was written to GCF_009192765.1_ASM919276v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:49,315] [INFO] DFAST_QC completed!
[2024-01-24 13:11:49,315] [INFO] Total running time: 0h2m20s