[2024-01-24 13:37:11,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:11,312] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:11,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference
[2024-01-24 13:37:12,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:12,604] [INFO] Task started: Prodigal
[2024-01-24 13:37:12,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgac1187a6-d407-4358-8bff-9eed76ef415b/GCF_019933155.2_ASM1993315v2_genomic.fna.gz | prodigal -d GCF_019933155.2_ASM1993315v2_genomic.fna/cds.fna -a GCF_019933155.2_ASM1993315v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:25,103] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:25,104] [INFO] Task started: HMMsearch
[2024-01-24 13:37:25,104] [INFO] Running command: hmmsearch --tblout GCF_019933155.2_ASM1993315v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/reference_markers.hmm GCF_019933155.2_ASM1993315v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:25,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:25,486] [INFO] Found 6/6 markers.
[2024-01-24 13:37:25,532] [INFO] Query marker FASTA was written to GCF_019933155.2_ASM1993315v2_genomic.fna/markers.fasta
[2024-01-24 13:37:25,532] [INFO] Task started: Blastn
[2024-01-24 13:37:25,533] [INFO] Running command: blastn -query GCF_019933155.2_ASM1993315v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/reference_markers.fasta -out GCF_019933155.2_ASM1993315v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:26,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:26,298] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:26,298] [INFO] Target genome list was writen to GCF_019933155.2_ASM1993315v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:26,314] [INFO] Task started: fastANI
[2024-01-24 13:37:26,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgac1187a6-d407-4358-8bff-9eed76ef415b/GCF_019933155.2_ASM1993315v2_genomic.fna.gz --refList GCF_019933155.2_ASM1993315v2_genomic.fna/target_genomes.txt --output GCF_019933155.2_ASM1993315v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:39,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:39,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:39,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:39,436] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:39,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:39,436] [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
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	100.0	1804	1804	95	conclusive
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	88.6096	1240	1804	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	88.6051	1230	1804	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	80.2944	630	1804	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	79.0907	235	1804	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	79.0643	146	1804	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	78.7591	103	1804	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	78.5191	161	1804	95	below_threshold
Bacillus methanolicus	strain=PB1	GCA_000262755.1	1471	1471	suspected-type	True	78.2883	96	1804	95	below_threshold
Bacillus pumilus	strain=ATCC 7061	GCA_000172815.1	1408	1408	suspected-type	True	78.1537	105	1804	95	below_threshold
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	77.4122	111	1804	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.3804	92	1804	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	77.1043	99	1804	95	below_threshold
Calidifontibacillus erzurumensis	strain=P2	GCA_013303125.1	2741433	2741433	type	True	76.7892	53	1804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:39,438] [INFO] DFAST Taxonomy check result was written to GCF_019933155.2_ASM1993315v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:39,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:39,438] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:39,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/checkm_data
[2024-01-24 13:37:39,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:39,493] [INFO] Task started: CheckM
[2024-01-24 13:37:39,494] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019933155.2_ASM1993315v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019933155.2_ASM1993315v2_genomic.fna/checkm_input GCF_019933155.2_ASM1993315v2_genomic.fna/checkm_result
[2024-01-24 13:38:20,468] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:20,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:20,492] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:20,493] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:20,493] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019933155.2_ASM1993315v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:20,494] [INFO] Task started: Blastn
[2024-01-24 13:38:20,494] [INFO] Running command: blastn -query GCF_019933155.2_ASM1993315v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg28b4934e-d1ff-4097-a806-6e1ae9fcaabf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019933155.2_ASM1993315v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:21,281] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:21,285] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:21,286] [INFO] Target genome list was writen to GCF_019933155.2_ASM1993315v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:21,305] [INFO] Task started: fastANI
[2024-01-24 13:38:21,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgac1187a6-d407-4358-8bff-9eed76ef415b/GCF_019933155.2_ASM1993315v2_genomic.fna.gz --refList GCF_019933155.2_ASM1993315v2_genomic.fna/target_genomes_gtdb.txt --output GCF_019933155.2_ASM1993315v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:36,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:36,075] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:36,076] [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_009674765.1	s__Bacillus_P idriensis	88.6053	1230	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.40	95.01	0.92	0.87	5	-
GCF_014235785.1	s__Bacillus_P sp002858905	82.691	882	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.85	98.20	0.93	0.90	4	-
GCF_000708755.2	s__Bacillus_P indicus	80.3011	629	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_003431975.1	s__Bacillus pumilus_N	79.3084	99	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.39	99.09	0.95	0.93	4	-
GCF_017497975.1	s__Metabacillus sp017497975	79.0979	235	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	78.9643	154	1804	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_003816055.1	s__Metabacillus_B sp003816055	78.6369	156	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018283675.1	s__Metabacillus_B sp018283675	78.4222	160	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773385.1	s__IB182487 sp014773385	78.3249	215	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__IB182487	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303275.1	s__Cytobacillus sp017303275	77.4277	143	1804	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_010093085.1	s__Bacillus sp010093085	77.3055	98	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744245.1	s__Bacillus pumilus_M	77.2951	84	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732485.2	s__Metabacillus_B sp000732485	77.1406	144	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691145.1	s__Bacillus altitudinis	77.1023	98	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.17	97.02	0.95	0.92	117	-
GCF_001592005.1	s__Bacillus sonorensis	77.0865	103	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.75	99.65	0.97	0.94	11	-
GCF_007678455.1	s__Mesobacillus oceanisediminis_A	77.0661	86	1804	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_001969855.1	s__Bacillus haynesii	77.0171	91	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_003315075.1	s__Rossellomorea aquimaris_C	76.966	81	1804	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	-
GCF_000300535.1	s__Bacillus xiamenensis	76.9493	94	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.27	99.24	0.95	0.94	4	-
GCF_013303125.1	s__Calidifontibacillus erzurumensis	76.7892	53	1804	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:36,077] [INFO] GTDB search result was written to GCF_019933155.2_ASM1993315v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:36,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:36,082] [INFO] DFAST_QC result json was written to GCF_019933155.2_ASM1993315v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:36,082] [INFO] DFAST_QC completed!
[2024-01-24 13:38:36,082] [INFO] Total running time: 0h1m25s