[2024-01-24 13:21:40,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,748] [INFO] DQC Reference Directory: /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference
[2024-01-24 13:21:42,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,065] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,066] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa8c3ed9-3255-444c-9fa5-26c8606daf8f/GCF_004340465.1_ASM434046v1_genomic.fna.gz | prodigal -d GCF_004340465.1_ASM434046v1_genomic.fna/cds.fna -a GCF_004340465.1_ASM434046v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:55,952] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:55,952] [INFO] Task started: HMMsearch
[2024-01-24 13:21:55,952] [INFO] Running command: hmmsearch --tblout GCF_004340465.1_ASM434046v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/reference_markers.hmm GCF_004340465.1_ASM434046v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:56,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:56,339] [INFO] Found 6/6 markers.
[2024-01-24 13:21:56,383] [INFO] Query marker FASTA was written to GCF_004340465.1_ASM434046v1_genomic.fna/markers.fasta
[2024-01-24 13:21:56,383] [INFO] Task started: Blastn
[2024-01-24 13:21:56,384] [INFO] Running command: blastn -query GCF_004340465.1_ASM434046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/reference_markers.fasta -out GCF_004340465.1_ASM434046v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:57,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:57,053] [INFO] Selected 18 target genomes.
[2024-01-24 13:21:57,053] [INFO] Target genome list was writen to GCF_004340465.1_ASM434046v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:57,061] [INFO] Task started: fastANI
[2024-01-24 13:21:57,061] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8c3ed9-3255-444c-9fa5-26c8606daf8f/GCF_004340465.1_ASM434046v1_genomic.fna.gz --refList GCF_004340465.1_ASM434046v1_genomic.fna/target_genomes.txt --output GCF_004340465.1_ASM434046v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:12,839] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:12,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:12,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:12,855] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:12,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:12,855] [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
Mesobacillus foraminis	strain=CV53	GCA_004340465.1	279826	279826	type	True	100.0	1892	1893	95	conclusive
Mesobacillus foraminis	strain=CV53	GCA_013618915.1	279826	279826	type	True	99.9979	1892	1893	95	conclusive
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	78.2721	343	1893	95	below_threshold
Peribacillus kribbensis	strain=DSM 17871	GCA_000430765.1	356658	356658	type	True	78.1427	109	1893	95	below_threshold
Mesobacillus subterraneus	strain=DSM 13966	GCA_003937825.1	285983	285983	suspected-type	True	77.701	218	1893	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.5205	134	1893	95	below_threshold
Mesobacillus zeae	strain=JJ-247	GCA_003570705.1	1917180	1917180	type	True	77.5059	213	1893	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	77.4089	65	1893	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	77.4008	93	1893	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	77.2659	148	1893	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.1908	127	1893	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.1564	106	1893	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	77.1264	127	1893	95	below_threshold
Falsibacillus pallidus	strain=DSM 25281	GCA_003350505.1	493781	493781	type	True	76.8047	88	1893	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	76.8035	117	1893	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_900094975.1	1402860	1402860	type	True	76.7937	78	1893	95	below_threshold
Bacillus enclensis	strain=SGD-1123	GCA_001456935.1	1402860	1402860	type	True	76.7899	79	1893	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	76.7025	51	1893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:12,860] [INFO] DFAST Taxonomy check result was written to GCF_004340465.1_ASM434046v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:12,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:12,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:12,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/checkm_data
[2024-01-24 13:22:12,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:12,922] [INFO] Task started: CheckM
[2024-01-24 13:22:12,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340465.1_ASM434046v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340465.1_ASM434046v1_genomic.fna/checkm_input GCF_004340465.1_ASM434046v1_genomic.fna/checkm_result
[2024-01-24 13:22:59,051] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:59,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,075] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:59,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:59,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340465.1_ASM434046v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:59,077] [INFO] Task started: Blastn
[2024-01-24 13:22:59,077] [INFO] Running command: blastn -query GCF_004340465.1_ASM434046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf895d821-2753-4526-a80e-ebc1454825ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340465.1_ASM434046v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:59,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:59,851] [INFO] Selected 24 target genomes.
[2024-01-24 13:22:59,852] [INFO] Target genome list was writen to GCF_004340465.1_ASM434046v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:59,862] [INFO] Task started: fastANI
[2024-01-24 13:22:59,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8c3ed9-3255-444c-9fa5-26c8606daf8f/GCF_004340465.1_ASM434046v1_genomic.fna.gz --refList GCF_004340465.1_ASM434046v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340465.1_ASM434046v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:18,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:18,539] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:18,540] [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_004340465.1	s__Bacillus_AZ foraminis	100.0	1892	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	97.82	96.47	0.93	0.88	4	conclusive
GCF_001273925.1	s__Bacillus_AZ sp001273925	78.5379	323	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000986785.1	s__Bacillus_AZ campisalis	78.2429	341	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424685.1	s__Mesobacillus boroniphilus_A	77.6935	191	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937825.1	s__Mesobacillus subterraneus	77.677	219	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613195.1	s__Mesobacillus sp018613195	77.658	201	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	98.95	98.95	0.85	0.85	2	-
GCF_016879755.1	s__Bacillus_AZ sp016879755	77.649	186	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014856545.1	s__Mesobacillus sp014856545	77.6477	213	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343535.1	s__Neobacillus sp018343535	77.5782	136	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_004366035.1	s__Cytobacillus oceanisediminis_C	77.5543	171	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003570705.1	s__Bacillus_AZ zeae	77.5059	213	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_AZ	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001038755.1	s__Cytobacillus firmus_B	77.467	151	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	77.3772	179	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
GCF_009849585.1	s__Cytobacillus sp009849585	77.2701	165	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956215.1	s__Cytobacillus sp001956215	77.2519	162	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002272225.1	s__Cytobacillus sp002272225	77.1646	144	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612665.1	s__Neobacillus dielmonensis	77.0939	130	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636345.1	s__Cytobacillus gottheilii	76.9267	129	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_001456935.1	s__Rossellomorea enclensis	76.8243	77	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	98.25	97.66	0.91	0.88	7	-
GCF_002561455.1	s__Rossellomorea sp002561455	76.6616	68	1893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_B;g__Rossellomorea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:18,541] [INFO] GTDB search result was written to GCF_004340465.1_ASM434046v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:18,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:18,545] [INFO] DFAST_QC result json was written to GCF_004340465.1_ASM434046v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:18,546] [INFO] DFAST_QC completed!
[2024-01-24 13:23:18,546] [INFO] Total running time: 0h1m38s