[2024-01-25 19:10:35,728] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:35,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:35,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference
[2024-01-25 19:10:36,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:36,909] [INFO] Task started: Prodigal
[2024-01-25 19:10:36,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c6ee41e-1aea-417d-9056-deb97c911b19/GCF_003852715.1_ASM385271v1_genomic.fna.gz | prodigal -d GCF_003852715.1_ASM385271v1_genomic.fna/cds.fna -a GCF_003852715.1_ASM385271v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:43,907] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:43,907] [INFO] Task started: HMMsearch
[2024-01-25 19:10:43,907] [INFO] Running command: hmmsearch --tblout GCF_003852715.1_ASM385271v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/reference_markers.hmm GCF_003852715.1_ASM385271v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:44,142] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:44,143] [INFO] Found 6/6 markers.
[2024-01-25 19:10:44,185] [INFO] Query marker FASTA was written to GCF_003852715.1_ASM385271v1_genomic.fna/markers.fasta
[2024-01-25 19:10:44,185] [INFO] Task started: Blastn
[2024-01-25 19:10:44,185] [INFO] Running command: blastn -query GCF_003852715.1_ASM385271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/reference_markers.fasta -out GCF_003852715.1_ASM385271v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:44,737] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:44,739] [INFO] Selected 23 target genomes.
[2024-01-25 19:10:44,740] [INFO] Target genome list was writen to GCF_003852715.1_ASM385271v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:44,754] [INFO] Task started: fastANI
[2024-01-25 19:10:44,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6ee41e-1aea-417d-9056-deb97c911b19/GCF_003852715.1_ASM385271v1_genomic.fna.gz --refList GCF_003852715.1_ASM385271v1_genomic.fna/target_genomes.txt --output GCF_003852715.1_ASM385271v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:00,655] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:00,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:00,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:00,668] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:00,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:00,668] [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
Ectobacillus antri	strain=SYSU K30001	GCA_003852715.1	2486280	2486280	type	True	100.0	1127	1131	95	conclusive
Ectobacillus panaciterrae	strain=DSM 19096	GCA_000430785.1	363872	363872	type	True	78.8369	315	1131	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	77.8333	192	1131	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	77.73	192	1131	95	below_threshold
Bacillus cereus	strain=FSL M8-0473	GCA_002014665.1	1396	1396	suspected-type	True	77.6912	181	1131	95	below_threshold
Niallia circulans	strain=NBRC 13626	GCA_001591585.1	1397	1397	suspected-type	True	77.6721	54	1131	95	below_threshold
Bacillus cereus	strain=ATCC 14579	GCA_006094295.1	1396	1396	suspected-type	True	77.6331	180	1131	95	below_threshold
Bacillus cereus	strain=NCTC2599	GCA_900445355.1	1396	1396	suspected-type	True	77.5926	179	1131	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.503	191	1131	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	77.4071	185	1131	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	77.3467	184	1131	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.3444	69	1131	95	below_threshold
Bacillus pacificus	strain=EB422	GCA_001884025.1	2026187	2026187	type	True	77.2632	183	1131	95	below_threshold
Bacillus luti	strain=TD41	GCA_001884105.1	2026191	2026191	type	True	77.2299	186	1131	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.0906	57	1131	95	below_threshold
Bacillus paranthracis	strain=Mn5	GCA_001883995.1	2026186	2026186	type	True	77.0382	195	1131	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	76.9933	79	1131	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.9244	100	1131	95	below_threshold
Bacillus taeanensis	strain=BH030017	GCA_003318295.1	273032	273032	type	True	76.8239	68	1131	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.7469	63	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:00,670] [INFO] DFAST Taxonomy check result was written to GCF_003852715.1_ASM385271v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:00,671] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:00,671] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:00,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/checkm_data
[2024-01-25 19:11:00,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:00,709] [INFO] Task started: CheckM
[2024-01-25 19:11:00,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003852715.1_ASM385271v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003852715.1_ASM385271v1_genomic.fna/checkm_input GCF_003852715.1_ASM385271v1_genomic.fna/checkm_result
[2024-01-25 19:11:26,202] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:26,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:26,226] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:26,226] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:26,226] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003852715.1_ASM385271v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:26,226] [INFO] Task started: Blastn
[2024-01-25 19:11:26,227] [INFO] Running command: blastn -query GCF_003852715.1_ASM385271v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3271f434-ca51-4b41-9ee2-887f64358107/dqc_reference/reference_markers_gtdb.fasta -out GCF_003852715.1_ASM385271v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:26,993] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:26,996] [INFO] Selected 25 target genomes.
[2024-01-25 19:11:26,996] [INFO] Target genome list was writen to GCF_003852715.1_ASM385271v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:27,011] [INFO] Task started: fastANI
[2024-01-25 19:11:27,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c6ee41e-1aea-417d-9056-deb97c911b19/GCF_003852715.1_ASM385271v1_genomic.fna.gz --refList GCF_003852715.1_ASM385271v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003852715.1_ASM385271v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:46,282] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:46,294] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:46,294] [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_003852715.1	s__Ectobacillus antri	100.0	1127	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430785.1	s__Ectobacillus panaciterrae	78.85	314	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Ectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116295.1	s__Bacillus_A sp900116295	77.9032	206	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112415.1	s__Bacillus_A sp900112415	77.8681	201	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.00	99.00	0.93	0.93	2	-
GCF_002551005.1	s__Bacillus_A pseudomycoides_C	77.8271	222	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590835.1	s__Bacillus_A gaemokensis	77.8166	193	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013314535.1	s__Bacillus_A sp013314535	77.7951	194	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.95	99.95	0.99	0.99	2	-
GCF_006384875.1	s__Bacillus_A bombysepticus	77.6576	178	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	97.0513	98.50	97.53	0.88	0.81	586	-
GCF_002200015.1	s__Bacillus_A cereus_AZ	77.5916	180	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.9563	N/A	N/A	N/A	N/A	1	-
GCA_002582035.1	s__Bacillus_A pseudomycoides_B	77.5901	219	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002561295.1	s__Bacillus_A cereus_S	77.5726	194	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.16	96.34	0.94	0.87	9	-
GCF_002560985.1	s__Bacillus_A sp002560985	77.5599	219	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832605.1	s__Bacillus_A mycoides	77.52	188	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.01	96.59	0.88	0.83	125	-
GCF_002975175.1	s__Bacillus_A sp002975175	77.491	179	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884135.1	s__Bacillus_A nitratireducens	77.3917	186	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.14	95.62	0.90	0.85	78	-
GCF_004340305.1	s__Gottfriedia sp004340305	77.0781	73	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	77.0485	59	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003184905.1	s__Priestia sp003184905	76.955	101	1131	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_016909075.1	s__Priestia iocasae	76.9244	100	1131	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_003318295.1	s__Maribacillus taeanensis	76.7235	67	1131	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__UBA6769;g__Maribacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:46,295] [INFO] GTDB search result was written to GCF_003852715.1_ASM385271v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:46,296] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:46,299] [INFO] DFAST_QC result json was written to GCF_003852715.1_ASM385271v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:46,299] [INFO] DFAST_QC completed!
[2024-01-25 19:11:46,299] [INFO] Total running time: 0h1m11s