[2024-01-25 19:34:21,098] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,099] [INFO] DQC Reference Directory: /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference
[2024-01-25 19:34:22,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,233] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,233] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c74ffcf-2bfa-4cf3-ae11-a37bdc57d50f/GCF_016908875.1_ASM1690887v1_genomic.fna.gz | prodigal -d GCF_016908875.1_ASM1690887v1_genomic.fna/cds.fna -a GCF_016908875.1_ASM1690887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:28,998] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:28,998] [INFO] Task started: HMMsearch
[2024-01-25 19:34:28,998] [INFO] Running command: hmmsearch --tblout GCF_016908875.1_ASM1690887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/reference_markers.hmm GCF_016908875.1_ASM1690887v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:29,217] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:29,218] [INFO] Found 6/6 markers.
[2024-01-25 19:34:29,246] [INFO] Query marker FASTA was written to GCF_016908875.1_ASM1690887v1_genomic.fna/markers.fasta
[2024-01-25 19:34:29,246] [INFO] Task started: Blastn
[2024-01-25 19:34:29,246] [INFO] Running command: blastn -query GCF_016908875.1_ASM1690887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/reference_markers.fasta -out GCF_016908875.1_ASM1690887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:29,781] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:29,784] [INFO] Selected 21 target genomes.
[2024-01-25 19:34:29,784] [INFO] Target genome list was writen to GCF_016908875.1_ASM1690887v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:29,789] [INFO] Task started: fastANI
[2024-01-25 19:34:29,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c74ffcf-2bfa-4cf3-ae11-a37bdc57d50f/GCF_016908875.1_ASM1690887v1_genomic.fna.gz --refList GCF_016908875.1_ASM1690887v1_genomic.fna/target_genomes.txt --output GCF_016908875.1_ASM1690887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:43,705] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:43,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:43,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:43,718] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:34:43,718] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:43,718] [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 ectoiniformans	strain=DSM 28970	GCA_016908875.1	1494429	1494429	type	True	100.0	1162	1163	95	conclusive
Bacillus aerolatus	strain=CX253	GCA_009183655.1	2653354	2653354	type	True	77.8901	231	1163	95	below_threshold
Bacillus wudalianchiensis	strain=FJAT-27215	GCA_001685015.1	1743143	1743143	type	True	77.7518	197	1163	95	below_threshold
Bacillus badius	strain=NBRC 15713	GCA_001591605.1	1455	1455	type	True	77.4064	198	1163	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	77.384	81	1163	95	below_threshold
Domibacillus enclensis	strain=NIO-1016	GCA_900156125.1	1017273	1017273	type	True	77.2121	97	1163	95	below_threshold
Domibacillus enclensis	strain=DSM 25145	GCA_002237775.1	1017273	1017273	type	True	77.1851	98	1163	95	below_threshold
Bacillus massiliglaciei	strain=Marseille-P2600	GCA_900098925.1	1816693	1816693	type	True	77.1557	64	1163	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_009720625.1	2567941	2567941	type	True	77.1312	67	1163	95	below_threshold
Domibacillus indicus	strain=SD 111	GCA_000970685.1	1437523	1437523	type	True	77.1033	107	1163	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.0553	59	1163	95	below_threshold
Metabacillus sediminilitoris	strain=DSL-17	GCA_004801455.1	2567941	2567941	type	True	76.9452	64	1163	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_000161615.1	1428	1428	suspected-type	True	76.944	56	1163	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	76.8827	62	1163	95	below_threshold
Priestia megaterium	strain=NBRC 15308	GCA_001591525.1	1404	1404	type	True	76.8234	72	1163	95	below_threshold
Priestia megaterium	strain=ATCC 14581	GCA_900113355.1	1404	1404	suspected-type	True	76.8144	75	1163	95	below_threshold
Bacillus coahuilensis	strain=m4-4	GCA_000171615.1	408580	408580	type	True	76.7749	66	1163	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	76.7508	67	1163	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	76.6484	64	1163	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	76.5238	62	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:43,720] [INFO] DFAST Taxonomy check result was written to GCF_016908875.1_ASM1690887v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:43,720] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:43,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:43,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/checkm_data
[2024-01-25 19:34:43,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:43,756] [INFO] Task started: CheckM
[2024-01-25 19:34:43,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908875.1_ASM1690887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908875.1_ASM1690887v1_genomic.fna/checkm_input GCF_016908875.1_ASM1690887v1_genomic.fna/checkm_result
[2024-01-25 19:35:08,500] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:08,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:08,518] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:08,519] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:08,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908875.1_ASM1690887v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:08,519] [INFO] Task started: Blastn
[2024-01-25 19:35:08,519] [INFO] Running command: blastn -query GCF_016908875.1_ASM1690887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf1f2b5-bfd0-4215-abb1-703b01e34fb2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908875.1_ASM1690887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:09,286] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:09,288] [INFO] Selected 24 target genomes.
[2024-01-25 19:35:09,289] [INFO] Target genome list was writen to GCF_016908875.1_ASM1690887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:09,304] [INFO] Task started: fastANI
[2024-01-25 19:35:09,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c74ffcf-2bfa-4cf3-ae11-a37bdc57d50f/GCF_016908875.1_ASM1690887v1_genomic.fna.gz --refList GCF_016908875.1_ASM1690887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908875.1_ASM1690887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:25,628] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:25,641] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:25,641] [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_016908875.1	s__Bacillus_BX ectoiniformans	100.0	1162	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Bacillus_BX	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002261155.1	s__FJAT-46582 sp002261155	78.0981	215	1163	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_002797375.1	s__FJAT-46582 sp002797375	78.027	243	1163	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	-
GCF_009183655.1	s__Pseudobacillus aerolatus	77.8816	231	1163	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_016820555.1	s__FJAT-46582 sp016820555	77.7537	227	1163	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_001685015.1	s__Pseudobacillus wudalianchiensis	77.7518	197	1163	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_003600835.1	s__Pseudobacillus sp003600835	77.5004	197	1163	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	77.4064	198	1163	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_002835735.1	s__Cytobacillus horneckiae	77.3895	80	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.87	98.22	0.90	0.90	3	-
GCF_008180335.1	s__Priestia megaterium_B	77.3579	64	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_H;g__Priestia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009849585.1	s__Cytobacillus sp009849585	77.2938	73	1163	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_007830235.1	s__Cytobacillus oceanisediminis	77.2501	92	1163	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_008923245.1	s__Cytobacillus depressus	77.2284	74	1163	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_900098925.1	s__Peribacillus massiliglaciei	77.1556	64	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756695.1	s__Heyndrickxia sporothermodurans	77.0608	69	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	99.73	97.95	0.95	0.84	38	-
GCF_000970685.1	s__Domibacillus indicus	77.0528	106	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333075.1	s__Heyndrickxia sporothermodurans_A	76.9396	72	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207535.1	s__Bacillus_BD benzoevorans	76.9315	67	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011393025.1	s__URHB0009 sp011393025	76.8739	51	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__URHB0009	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000171615.1	s__Bacillus_T coahuilensis	76.8378	66	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_K;g__Bacillus_T	95.0	98.94	98.61	0.92	0.90	3	-
GCF_002272225.1	s__Cytobacillus sp002272225	76.6376	77	1163	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_019039215.1	s__Cytobacillus sp019039215	76.5589	82	1163	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	-
GCA_017656295.1	s__JACDOC01 sp017656295	76.5313	77	1163	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:25,643] [INFO] GTDB search result was written to GCF_016908875.1_ASM1690887v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:25,643] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:25,647] [INFO] DFAST_QC result json was written to GCF_016908875.1_ASM1690887v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:25,647] [INFO] DFAST_QC completed!
[2024-01-25 19:35:25,647] [INFO] Total running time: 0h1m5s