[2024-01-25 19:49:05,608] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:49:05,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:49:05,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference
[2024-01-25 19:49:06,745] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:49:06,745] [INFO] Task started: Prodigal
[2024-01-25 19:49:06,746] [INFO] Running command: gunzip -c /var/lib/cwl/stge7caa8f3-1573-4cea-9148-ac73813202e7/GCF_002797355.1_ASM279735v1_genomic.fna.gz | prodigal -d GCF_002797355.1_ASM279735v1_genomic.fna/cds.fna -a GCF_002797355.1_ASM279735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:49:13,718] [INFO] Task succeeded: Prodigal
[2024-01-25 19:49:13,718] [INFO] Task started: HMMsearch
[2024-01-25 19:49:13,718] [INFO] Running command: hmmsearch --tblout GCF_002797355.1_ASM279735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/reference_markers.hmm GCF_002797355.1_ASM279735v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:49:13,922] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:49:13,923] [INFO] Found 6/6 markers.
[2024-01-25 19:49:13,949] [INFO] Query marker FASTA was written to GCF_002797355.1_ASM279735v1_genomic.fna/markers.fasta
[2024-01-25 19:49:13,950] [INFO] Task started: Blastn
[2024-01-25 19:49:13,950] [INFO] Running command: blastn -query GCF_002797355.1_ASM279735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/reference_markers.fasta -out GCF_002797355.1_ASM279735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:14,492] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:14,495] [INFO] Selected 26 target genomes.
[2024-01-25 19:49:14,495] [INFO] Target genome list was writen to GCF_002797355.1_ASM279735v1_genomic.fna/target_genomes.txt
[2024-01-25 19:49:14,509] [INFO] Task started: fastANI
[2024-01-25 19:49:14,509] [INFO] Running command: fastANI --query /var/lib/cwl/stge7caa8f3-1573-4cea-9148-ac73813202e7/GCF_002797355.1_ASM279735v1_genomic.fna.gz --refList GCF_002797355.1_ASM279735v1_genomic.fna/target_genomes.txt --output GCF_002797355.1_ASM279735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:49:30,711] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:30,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:49:30,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:49:30,721] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:49:30,721] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:49:30,721] [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
Bacillus xiapuensis	strain=FJAT-46582	GCA_002797355.1	2014075	2014075	type	True	100.0	1083	1087	95	conclusive
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	80.7657	68	1087	95	below_threshold
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	79.6894	56	1087	95	below_threshold
Bacillus thermotolerans	strain=SGZ-8	GCA_000812025.2	1221996	1221996	type	True	78.752	160	1087	95	below_threshold
Bacillus thermotolerans	strain=SgZ-8	GCA_011751085.1	1221996	1221996	type	True	78.6688	160	1087	95	below_threshold
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	78.0161	256	1087	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	77.9046	60	1087	95	below_threshold
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	77.8378	225	1087	95	below_threshold
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	77.7605	233	1087	95	below_threshold
Mesobacillus campisalis	strain=SA2-6	GCA_000986785.1	1408103	1408103	type	True	77.7416	54	1087	95	below_threshold
Bacillus halotolerans	strain=ATCC 25096	GCA_001517105.1	260554	260554	type	True	77.2804	51	1087	95	below_threshold
Domibacillus mangrovi	strain=SAOS 44	GCA_001906925.1	1714354	1714354	type	True	77.2791	74	1087	95	below_threshold
Domibacillus tundrae	strain=PAMC 80007	GCA_000970675.1	1587527	1587527	type	True	77.0837	77	1087	95	below_threshold
Domibacillus antri	strain=XD80	GCA_001936625.1	1714264	1714264	type	True	76.9757	103	1087	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	76.748	69	1087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:49:30,723] [INFO] DFAST Taxonomy check result was written to GCF_002797355.1_ASM279735v1_genomic.fna/tc_result.tsv
[2024-01-25 19:49:30,723] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:49:30,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:49:30,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/checkm_data
[2024-01-25 19:49:30,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:49:30,757] [INFO] Task started: CheckM
[2024-01-25 19:49:30,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002797355.1_ASM279735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002797355.1_ASM279735v1_genomic.fna/checkm_input GCF_002797355.1_ASM279735v1_genomic.fna/checkm_result
[2024-01-25 19:49:55,916] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:55,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:55,934] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:55,934] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:55,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002797355.1_ASM279735v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:55,934] [INFO] Task started: Blastn
[2024-01-25 19:49:55,935] [INFO] Running command: blastn -query GCF_002797355.1_ASM279735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebcf618b-5ea7-4791-bdfb-0ea10fae523d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002797355.1_ASM279735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:56,749] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:56,752] [INFO] Selected 24 target genomes.
[2024-01-25 19:49:56,752] [INFO] Target genome list was writen to GCF_002797355.1_ASM279735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:56,782] [INFO] Task started: fastANI
[2024-01-25 19:49:56,782] [INFO] Running command: fastANI --query /var/lib/cwl/stge7caa8f3-1573-4cea-9148-ac73813202e7/GCF_002797355.1_ASM279735v1_genomic.fna.gz --refList GCF_002797355.1_ASM279735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002797355.1_ASM279735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:14,194] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:14,206] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:14,206] [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_002797355.1	s__FJAT-46582 sp002797355	100.0	1086	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001636345.1	s__Cytobacillus gottheilii	79.5325	82	1087	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_000632515.1	s__Saccharococcus sp000632515	79.3974	54	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003600835.1	s__Pseudobacillus sp003600835	79.0635	215	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797375.1	s__FJAT-46582 sp002797375	78.9532	321	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	96.55	96.55	0.91	0.91	2	-
GCA_002261155.1	s__FJAT-46582 sp002261155	78.7914	286	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812025.2	s__Quasibacillus thermotolerans	78.752	160	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Quasibacillus	95.0	99.41	99.00	0.94	0.91	4	-
GCF_016820555.1	s__FJAT-46582 sp016820555	78.5896	321	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__FJAT-46582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183655.1	s__Pseudobacillus aerolatus	78.0716	257	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591605.1	s__Pseudobacillus badius	77.7883	233	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	98.55	97.77	0.93	0.89	8	-
GCF_001685015.1	s__Pseudobacillus wudalianchiensis	77.7774	223	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_001906925.1	s__Domibacillus mangrovi	77.3965	75	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830235.1	s__Cytobacillus oceanisediminis	77.3492	70	1087	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_003182355.1	s__Cytobacillus oceanisediminis_A	77.2636	65	1087	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_000970675.1	s__Domibacillus tundrae	77.1123	77	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935355.1	s__Rossellomorea aquimaris_B	77.0168	53	1087	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_001936625.1	s__Domibacillus antri	77.0004	102	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613055.1	s__Mesobacillus sp018613055	76.8805	62	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008923245.1	s__Cytobacillus depressus	76.7447	68	1087	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_001591565.1	s__Priestia flexa	76.4076	52	1087	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	99.12	98.83	0.89	0.87	15	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:14,207] [INFO] GTDB search result was written to GCF_002797355.1_ASM279735v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:14,208] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:14,211] [INFO] DFAST_QC result json was written to GCF_002797355.1_ASM279735v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:14,211] [INFO] DFAST_QC completed!
[2024-01-25 19:50:14,211] [INFO] Total running time: 0h1m9s