[2024-01-24 12:14:09,431] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:09,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:09,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference
[2024-01-24 12:14:10,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:10,828] [INFO] Task started: Prodigal
[2024-01-24 12:14:10,828] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbc96f73-a36e-4062-b11b-37409ab08e7f/GCF_009728145.1_ASM972814v1_genomic.fna.gz | prodigal -d GCF_009728145.1_ASM972814v1_genomic.fna/cds.fna -a GCF_009728145.1_ASM972814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:18,935] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:18,936] [INFO] Task started: HMMsearch
[2024-01-24 12:14:18,936] [INFO] Running command: hmmsearch --tblout GCF_009728145.1_ASM972814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/reference_markers.hmm GCF_009728145.1_ASM972814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:19,323] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:19,325] [INFO] Found 6/6 markers.
[2024-01-24 12:14:19,359] [INFO] Query marker FASTA was written to GCF_009728145.1_ASM972814v1_genomic.fna/markers.fasta
[2024-01-24 12:14:19,359] [INFO] Task started: Blastn
[2024-01-24 12:14:19,360] [INFO] Running command: blastn -query GCF_009728145.1_ASM972814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/reference_markers.fasta -out GCF_009728145.1_ASM972814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:19,959] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:19,962] [INFO] Selected 27 target genomes.
[2024-01-24 12:14:19,963] [INFO] Target genome list was writen to GCF_009728145.1_ASM972814v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:19,978] [INFO] Task started: fastANI
[2024-01-24 12:14:19,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc96f73-a36e-4062-b11b-37409ab08e7f/GCF_009728145.1_ASM972814v1_genomic.fna.gz --refList GCF_009728145.1_ASM972814v1_genomic.fna/target_genomes.txt --output GCF_009728145.1_ASM972814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:36,587] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:36,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:36,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:36,604] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:36,604] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:36,604] [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
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	78.4302	286	1366	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	78.0377	221	1366	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.9569	213	1366	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	77.6666	234	1366	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.5924	201	1366	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	77.4669	197	1366	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.4611	212	1366	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.4219	147	1366	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.3574	146	1366	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.2985	184	1366	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.279	165	1366	95	below_threshold
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	77.2377	144	1366	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.2304	168	1366	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.2103	198	1366	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	77.0897	94	1366	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	76.9555	81	1366	95	below_threshold
Virgibacillus chiguensis	strain=CGMCC 1.6496	GCA_900129865.1	411959	411959	type	True	76.8171	131	1366	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	76.6225	53	1366	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.4239	51	1366	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	76.3488	68	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:36,612] [INFO] DFAST Taxonomy check result was written to GCF_009728145.1_ASM972814v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:36,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:36,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:36,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/checkm_data
[2024-01-24 12:14:36,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:36,665] [INFO] Task started: CheckM
[2024-01-24 12:14:36,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009728145.1_ASM972814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009728145.1_ASM972814v1_genomic.fna/checkm_input GCF_009728145.1_ASM972814v1_genomic.fna/checkm_result
[2024-01-24 12:15:06,830] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:06,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,855] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:06,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:06,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009728145.1_ASM972814v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:06,856] [INFO] Task started: Blastn
[2024-01-24 12:15:06,856] [INFO] Running command: blastn -query GCF_009728145.1_ASM972814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa741bce-b242-4f84-8a03-98f1ed91168d/dqc_reference/reference_markers_gtdb.fasta -out GCF_009728145.1_ASM972814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:07,622] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:07,626] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:07,626] [INFO] Target genome list was writen to GCF_009728145.1_ASM972814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:07,645] [INFO] Task started: fastANI
[2024-01-24 12:15:07,646] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc96f73-a36e-4062-b11b-37409ab08e7f/GCF_009728145.1_ASM972814v1_genomic.fna.gz --refList GCF_009728145.1_ASM972814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009728145.1_ASM972814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:22,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:22,606] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:22,606] [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_009728145.1	s__Ornithinibacillus caprae	100.0	1362	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111445.1	s__Ornithinibacillus limi	79.3458	468	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	78.435	287	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038425.2	s__Ornithinibacillus contaminans	78.0377	221	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038485.1	s__Ornithinibacillus californiensis	77.9181	217	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018310345.1	s__Ornithinibacillus massiliensis	77.6934	232	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	99.20	99.20	0.97	0.97	2	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	77.6231	229	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	77.5954	219	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	77.5889	202	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	77.4611	212	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993955.1	s__YIM-98839 sp010993955	77.4534	197	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369575.1	s__Oceanobacillus arenosus	77.4054	147	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	77.3539	192	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_900176885.1	s__Oceanobacillus senegalensis	77.2773	166	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002287375.1	s__Virgibacillus_G profundi	77.2081	199	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	76.9847	80	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_018333215.1	s__Oceanobacillus sp018333215	76.8985	109	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667825.1	s__Metabacillus litoralis_B	76.8239	77	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	98.61	98.61	0.90	0.90	2	-
GCF_009858175.1	s__Pontibacillus sp009858175	76.5167	69	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:22,608] [INFO] GTDB search result was written to GCF_009728145.1_ASM972814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:22,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:22,615] [INFO] DFAST_QC result json was written to GCF_009728145.1_ASM972814v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:22,615] [INFO] DFAST_QC completed!
[2024-01-24 12:15:22,616] [INFO] Total running time: 0h1m13s