[2024-01-24 12:22:34,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,056] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,057] [INFO] DQC Reference Directory: /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference
[2024-01-24 12:22:35,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,716] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgf79025a7-7ad3-4a71-8006-e1faae095789/GCF_004347775.1_ASM434777v1_genomic.fna.gz | prodigal -d GCF_004347775.1_ASM434777v1_genomic.fna/cds.fna -a GCF_004347775.1_ASM434777v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:01,810] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:01,810] [INFO] Task started: HMMsearch
[2024-01-24 12:23:01,811] [INFO] Running command: hmmsearch --tblout GCF_004347775.1_ASM434777v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/reference_markers.hmm GCF_004347775.1_ASM434777v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:02,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:02,090] [INFO] Found 6/6 markers.
[2024-01-24 12:23:02,130] [INFO] Query marker FASTA was written to GCF_004347775.1_ASM434777v1_genomic.fna/markers.fasta
[2024-01-24 12:23:02,131] [INFO] Task started: Blastn
[2024-01-24 12:23:02,131] [INFO] Running command: blastn -query GCF_004347775.1_ASM434777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/reference_markers.fasta -out GCF_004347775.1_ASM434777v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:02,707] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:02,712] [INFO] Selected 21 target genomes.
[2024-01-24 12:23:02,712] [INFO] Target genome list was writen to GCF_004347775.1_ASM434777v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:02,733] [INFO] Task started: fastANI
[2024-01-24 12:23:02,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgf79025a7-7ad3-4a71-8006-e1faae095789/GCF_004347775.1_ASM434777v1_genomic.fna.gz --refList GCF_004347775.1_ASM434777v1_genomic.fna/target_genomes.txt --output GCF_004347775.1_ASM434777v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:19,961] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:19,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:19,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:19,972] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:19,972] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:19,973] [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
Cnuella takakiae	strain=RG1-1	GCA_001953305.1	1302690	1302690	type	True	78.2765	568	1601	95	below_threshold
Cnuella takakiae	strain=DSM 26897	GCA_900129015.1	1302690	1302690	type	True	78.1863	578	1601	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	77.067	87	1601	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	76.8914	137	1601	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.8606	56	1601	95	below_threshold
Flavisolibacter nicotianae	strain=X7X	GCA_003628535.1	2364882	2364882	type	True	76.7918	237	1601	95	below_threshold
Flaviaesturariibacter flavus	strain=17J68-12	GCA_004337505.1	2502780	2502780	type	True	76.6702	166	1601	95	below_threshold
Flavisolibacter ginsenosidimutans	strain=Gsoil 636	GCA_007970805.1	661481	661481	type	True	76.6015	187	1601	95	below_threshold
Flaviaesturariibacter aridisoli	strain=17J68-15	GCA_004343705.1	2545761	2545761	type	True	76.4794	176	1601	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.4324	61	1601	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.4129	58	1601	95	below_threshold
Pseudobacter ginsenosidimutans	strain=Gsoil 221	GCA_007970185.1	661488	661488	type	True	76.3329	88	1601	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	76.29	110	1601	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	76.1803	109	1601	95	below_threshold
Pseudobacter ginsenosidimutans	strain=DSM 18116	GCA_004291315.1	661488	661488	type	True	75.9719	86	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:19,981] [INFO] DFAST Taxonomy check result was written to GCF_004347775.1_ASM434777v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:19,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:19,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:19,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/checkm_data
[2024-01-24 12:23:19,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:20,032] [INFO] Task started: CheckM
[2024-01-24 12:23:20,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004347775.1_ASM434777v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004347775.1_ASM434777v1_genomic.fna/checkm_input GCF_004347775.1_ASM434777v1_genomic.fna/checkm_result
[2024-01-24 12:24:27,536] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:27,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:27,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:27,556] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:27,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004347775.1_ASM434777v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:27,556] [INFO] Task started: Blastn
[2024-01-24 12:24:27,556] [INFO] Running command: blastn -query GCF_004347775.1_ASM434777v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2639c23-adeb-4c28-b572-aaad8dd27b79/dqc_reference/reference_markers_gtdb.fasta -out GCF_004347775.1_ASM434777v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:28,326] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:28,329] [INFO] Selected 15 target genomes.
[2024-01-24 12:24:28,329] [INFO] Target genome list was writen to GCF_004347775.1_ASM434777v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:28,340] [INFO] Task started: fastANI
[2024-01-24 12:24:28,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgf79025a7-7ad3-4a71-8006-e1faae095789/GCF_004347775.1_ASM434777v1_genomic.fna.gz --refList GCF_004347775.1_ASM434777v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004347775.1_ASM434777v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:41,908] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:41,917] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:41,918] [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_003332885.2	s__Paracnuella aquatica	95.5445	1478	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paracnuella	95.0	95.63	95.63	0.92	0.92	2	conclusive
GCF_001953305.1	s__Cnuella takakiae	78.291	568	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Cnuella	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013327885.1	s__Flavisolibacter sp013327885	77.8066	327	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.9803	255	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009740285.1	s__Phnomibacter ginsenosidimutans	76.9272	137	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Phnomibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628535.1	s__Flavisolibacter nicotianae	76.7918	237	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337505.1	s__Flaviaesturariibacter flavus	76.7199	167	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970805.1	s__Flavisolibacter ginsenosidimutans	76.6015	187	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343705.1	s__Flaviaesturariibacter aridisoli	76.4617	175	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flaviaesturariibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.3924	87	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_900110245.1	s__Niastella yeongjuensis	76.1803	109	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001898485.1	s__46-32 sp001898485	76.0012	93	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32	95.0	99.14	98.30	0.96	0.92	3	-
GCA_016786725.1	s__Ferruginibacter sp016786725	75.8228	58	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001896965.1	s__Niabella sp001896965	75.3442	51	1601	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:41,919] [INFO] GTDB search result was written to GCF_004347775.1_ASM434777v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:41,920] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:41,923] [INFO] DFAST_QC result json was written to GCF_004347775.1_ASM434777v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:41,923] [INFO] DFAST_QC completed!
[2024-01-24 12:24:41,923] [INFO] Total running time: 0h2m8s