[2024-01-24 12:39:35,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,029] [INFO] DQC Reference Directory: /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference
[2024-01-24 12:39:36,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,259] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,259] [INFO] Running command: gunzip -c /var/lib/cwl/stg1071de16-b166-494a-91ff-1adfd9007871/GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/cds.fna -a GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:42,579] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:42,579] [INFO] Task started: HMMsearch
[2024-01-24 12:39:42,580] [INFO] Running command: hmmsearch --tblout GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/reference_markers.hmm GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:42,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:42,841] [INFO] Found 6/6 markers.
[2024-01-24 12:39:42,872] [INFO] Query marker FASTA was written to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:39:42,872] [INFO] Task started: Blastn
[2024-01-24 12:39:42,872] [INFO] Running command: blastn -query GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/reference_markers.fasta -out GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:43,463] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:43,468] [INFO] Selected 18 target genomes.
[2024-01-24 12:39:43,469] [INFO] Target genome list was writen to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:39:43,484] [INFO] Task started: fastANI
[2024-01-24 12:39:43,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg1071de16-b166-494a-91ff-1adfd9007871/GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna.gz --refList GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:39:54,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:54,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:39:54,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:39:54,304] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:39:54,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:39:54,305] [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	100.0	1095	1103	95	conclusive
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.8815	238	1103	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	77.8682	186	1103	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.8242	177	1103	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.5895	186	1103	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.4364	166	1103	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	77.1537	171	1103	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.1311	165	1103	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.8865	143	1103	95	below_threshold
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	76.5498	115	1103	95	below_threshold
Lottiidibacillus patelloidae	strain=SA5d-4	GCA_002262935.1	2670334	2670334	type	True	76.5298	57	1103	95	below_threshold
Paraliobacillus sediminis	strain=126C4	GCA_003426055.1	1885916	1885916	type	True	76.2584	63	1103	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.1103	56	1103	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	75.9909	51	1103	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:39:54,306] [INFO] DFAST Taxonomy check result was written to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:39:54,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:39:54,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:39:54,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/checkm_data
[2024-01-24 12:39:54,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:39:54,348] [INFO] Task started: CheckM
[2024-01-24 12:39:54,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/checkm_input GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:40:20,259] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:20,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:20,287] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:20,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:20,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:40:20,289] [INFO] Task started: Blastn
[2024-01-24 12:40:20,290] [INFO] Running command: blastn -query GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0896f6e6-de6d-4e95-9a21-935e1e3485e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:21,131] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:21,135] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:21,135] [INFO] Target genome list was writen to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:21,146] [INFO] Task started: fastANI
[2024-01-24 12:40:21,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg1071de16-b166-494a-91ff-1adfd9007871/GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna.gz --refList GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:32,620] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:32,632] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:32,633] [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_900129485.1	s__Ornithinibacillus halophilus	100.0	1095	1103	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_009728145.1	s__Ornithinibacillus caprae	78.3552	299	1103	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_900111445.1	s__Ornithinibacillus limi	78.1618	256	1103	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	77.9295	238	1103	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	77.8909	207	1103	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	77.8664	188	1103	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_001038425.2	s__Ornithinibacillus contaminans	77.81	177	1103	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_018333235.1	s__Ornithinibacillus bavariensis	77.677	151	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	98.72	98.72	0.93	0.93	2	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	77.5865	213	1103	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	77.5839	185	1103	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_014638995.1	s__Virgibacillus_E oceani	77.2932	138	1103	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_014905415.1	s__Virgibacillus salexigens	77.1571	143	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_010993955.1	s__YIM-98839 sp010993955	77.137	173	1103	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_003515705.1	s__Oceanobacillus profundus	77.0641	143	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_017873675.1	s__Lentibacillus litoralis	76.9031	142	1103	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:32,636] [INFO] GTDB search result was written to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:32,638] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:32,642] [INFO] DFAST_QC result json was written to GCF_900129485.1_IMG-taxon_2654588106_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:40:32,642] [INFO] DFAST_QC completed!
[2024-01-24 12:40:32,642] [INFO] Total running time: 0h0m58s