[2024-01-24 12:23:51,029] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:51,031] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:51,032] [INFO] DQC Reference Directory: /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference
[2024-01-24 12:23:52,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:52,367] [INFO] Task started: Prodigal
[2024-01-24 12:23:52,367] [INFO] Running command: gunzip -c /var/lib/cwl/stg76777ef2-71db-4a4a-bf9e-91d6a4635b9d/GCF_003665065.1_ASM366506v1_genomic.fna.gz | prodigal -d GCF_003665065.1_ASM366506v1_genomic.fna/cds.fna -a GCF_003665065.1_ASM366506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:00,397] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:00,398] [INFO] Task started: HMMsearch
[2024-01-24 12:24:00,398] [INFO] Running command: hmmsearch --tblout GCF_003665065.1_ASM366506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/reference_markers.hmm GCF_003665065.1_ASM366506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:00,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:00,669] [INFO] Found 6/6 markers.
[2024-01-24 12:24:00,705] [INFO] Query marker FASTA was written to GCF_003665065.1_ASM366506v1_genomic.fna/markers.fasta
[2024-01-24 12:24:00,705] [INFO] Task started: Blastn
[2024-01-24 12:24:00,706] [INFO] Running command: blastn -query GCF_003665065.1_ASM366506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/reference_markers.fasta -out GCF_003665065.1_ASM366506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:01,301] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:01,304] [INFO] Selected 31 target genomes.
[2024-01-24 12:24:01,305] [INFO] Target genome list was writen to GCF_003665065.1_ASM366506v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:01,316] [INFO] Task started: fastANI
[2024-01-24 12:24:01,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg76777ef2-71db-4a4a-bf9e-91d6a4635b9d/GCF_003665065.1_ASM366506v1_genomic.fna.gz --refList GCF_003665065.1_ASM366506v1_genomic.fna/target_genomes.txt --output GCF_003665065.1_ASM366506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:17,921] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:17,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:17,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:17,940] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:17,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:17,941] [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
Oceanobacillus piezotolerans	strain=YLB-02	GCA_003665065.1	2448030	2448030	type	True	100.0	1319	1321	95	conclusive
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.7375	220	1321	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.773	251	1321	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	77.6724	142	1321	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.6532	237	1321	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.632	102	1321	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.5411	216	1321	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.4374	104	1321	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	77.3838	118	1321	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.2191	111	1321	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.2158	105	1321	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.204	115	1321	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.0606	108	1321	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	76.8542	153	1321	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.7934	95	1321	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.545	105	1321	95	below_threshold
Gracilibacillus boraciitolerans	strain=JCM 21714	GCA_000521485.1	307521	307521	type	True	76.5035	53	1321	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	76.2045	52	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:17,942] [INFO] DFAST Taxonomy check result was written to GCF_003665065.1_ASM366506v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:17,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:17,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:17,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/checkm_data
[2024-01-24 12:24:17,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:17,989] [INFO] Task started: CheckM
[2024-01-24 12:24:17,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003665065.1_ASM366506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003665065.1_ASM366506v1_genomic.fna/checkm_input GCF_003665065.1_ASM366506v1_genomic.fna/checkm_result
[2024-01-24 12:24:47,117] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:47,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:47,139] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:47,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:47,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003665065.1_ASM366506v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:47,140] [INFO] Task started: Blastn
[2024-01-24 12:24:47,140] [INFO] Running command: blastn -query GCF_003665065.1_ASM366506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg201fe583-55c2-439e-95f2-ccdfeea85911/dqc_reference/reference_markers_gtdb.fasta -out GCF_003665065.1_ASM366506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:47,935] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:47,938] [INFO] Selected 29 target genomes.
[2024-01-24 12:24:47,939] [INFO] Target genome list was writen to GCF_003665065.1_ASM366506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:47,959] [INFO] Task started: fastANI
[2024-01-24 12:24:47,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg76777ef2-71db-4a4a-bf9e-91d6a4635b9d/GCF_003665065.1_ASM366506v1_genomic.fna.gz --refList GCF_003665065.1_ASM366506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003665065.1_ASM366506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:05,498] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:05,525] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:05,526] [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_003665065.1	s__Oceanobacillus piezotolerans	100.0	1319	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003352005.1	s__Oceanobacillus zhaokaii	78.7388	225	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_001659985.1	s__Oceanobacillus sp001659985	77.9776	187	1321	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_003628445.1	s__Oceanobacillus bengalensis	77.7615	251	1321	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_001618145.1	s__Oceanobacillus damuensis	77.673	142	1321	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_000577245.1	s__Ornithinibacillus sp000577245	77.6554	128	1321	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_009733865.1	s__Oceanobacillus salinisoli	77.654	239	1321	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_001038425.2	s__Ornithinibacillus contaminans	77.5716	104	1321	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	77.3838	118	1321	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_000011245.1	s__Oceanobacillus iheyensis	77.2158	105	1321	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_000190475.1	s__Ornithinibacillus scapharcae	77.1841	114	1321	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_000482485.1	s__Ornithinibacillus globulus	77.1705	126	1321	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_900258515.1	s__Virgibacillus_E sp900258515	77.166	113	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	77.1297	114	1321	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_018075365.1	s__Virgibacillus pantothenticus	76.876	103	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_018916875.1	s__Virgibacillus proomii_B	76.5365	90	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521485.1	s__Gracilibacillus boraciitolerans	76.5035	53	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900626275.1	s__Gracilibacillus phocaeensis	76.3267	50	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	99.02	99.02	0.89	0.89	3	-
GCF_014646635.1	s__Lentibacillus kapialis	76.3095	54	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	76.2483	52	1321	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:05,528] [INFO] GTDB search result was written to GCF_003665065.1_ASM366506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:05,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:05,533] [INFO] DFAST_QC result json was written to GCF_003665065.1_ASM366506v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:05,534] [INFO] DFAST_QC completed!
[2024-01-24 12:25:05,534] [INFO] Total running time: 0h1m15s