[2024-01-24 11:27:19,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,201] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference
[2024-01-24 11:27:20,408] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,409] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg2df0e357-9360-4417-bd91-a332e1533431/GCF_008039555.1_ASM803955v1_genomic.fna.gz | prodigal -d GCF_008039555.1_ASM803955v1_genomic.fna/cds.fna -a GCF_008039555.1_ASM803955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:26,485] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:26,485] [INFO] Task started: HMMsearch
[2024-01-24 11:27:26,485] [INFO] Running command: hmmsearch --tblout GCF_008039555.1_ASM803955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/reference_markers.hmm GCF_008039555.1_ASM803955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:26,755] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:26,756] [INFO] Found 6/6 markers.
[2024-01-24 11:27:26,782] [INFO] Query marker FASTA was written to GCF_008039555.1_ASM803955v1_genomic.fna/markers.fasta
[2024-01-24 11:27:26,782] [INFO] Task started: Blastn
[2024-01-24 11:27:26,782] [INFO] Running command: blastn -query GCF_008039555.1_ASM803955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/reference_markers.fasta -out GCF_008039555.1_ASM803955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:27,379] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:27,383] [INFO] Selected 25 target genomes.
[2024-01-24 11:27:27,384] [INFO] Target genome list was writen to GCF_008039555.1_ASM803955v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:27,493] [INFO] Task started: fastANI
[2024-01-24 11:27:27,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df0e357-9360-4417-bd91-a332e1533431/GCF_008039555.1_ASM803955v1_genomic.fna.gz --refList GCF_008039555.1_ASM803955v1_genomic.fna/target_genomes.txt --output GCF_008039555.1_ASM803955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:41,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:41,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:41,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:41,714] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:41,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:41,715] [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
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	100.0	1006	1006	95	conclusive
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	78.1166	98	1006	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	78.1136	251	1006	95	below_threshold
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	78.036	243	1006	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	77.56	127	1006	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.9541	110	1006	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.8592	91	1006	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.7196	116	1006	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	76.6037	101	1006	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	76.6004	119	1006	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.5555	98	1006	95	below_threshold
Gracilibacillus kekensis	strain=CGMCC 1.10681	GCA_900143085.1	1027249	1027249	type	True	76.5183	52	1006	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.4748	62	1006	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	76.46	88	1006	95	below_threshold
Paraliobacillus ryukyuensis	strain=DSM 15140	GCA_003315295.1	200904	200904	type	True	76.3841	78	1006	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.0615	52	1006	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	76.0448	78	1006	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	76.0448	78	1006	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	75.7258	51	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:41,716] [INFO] DFAST Taxonomy check result was written to GCF_008039555.1_ASM803955v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:41,716] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:41,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:41,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/checkm_data
[2024-01-24 11:27:41,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:41,750] [INFO] Task started: CheckM
[2024-01-24 11:27:41,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008039555.1_ASM803955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008039555.1_ASM803955v1_genomic.fna/checkm_input GCF_008039555.1_ASM803955v1_genomic.fna/checkm_result
[2024-01-24 11:28:06,239] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:06,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:06,258] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:06,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:06,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008039555.1_ASM803955v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:06,259] [INFO] Task started: Blastn
[2024-01-24 11:28:06,260] [INFO] Running command: blastn -query GCF_008039555.1_ASM803955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74f1de43-c3e1-44d3-b06d-78f8dede8802/dqc_reference/reference_markers_gtdb.fasta -out GCF_008039555.1_ASM803955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:07,012] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:07,015] [INFO] Selected 24 target genomes.
[2024-01-24 11:28:07,015] [INFO] Target genome list was writen to GCF_008039555.1_ASM803955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:07,035] [INFO] Task started: fastANI
[2024-01-24 11:28:07,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df0e357-9360-4417-bd91-a332e1533431/GCF_008039555.1_ASM803955v1_genomic.fna.gz --refList GCF_008039555.1_ASM803955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008039555.1_ASM803955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:21,152] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:21,173] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:21,174] [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_008039555.1	s__Cerasibacillus terrae	100.0	1006	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	99.05	99.05	0.92	0.92	2	conclusive
GCF_014202495.1	s__Cerasibacillus quisquiliarum	78.1287	250	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014637405.1	s__Ornithinibacillus halotolerans	77.5454	129	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	77.0344	96	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCA_014642895.1	s__Virgibacillus_E populi	76.9827	90	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	98.98	98.88	0.86	0.85	5	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.9534	110	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482485.1	s__Ornithinibacillus globulus	76.8615	107	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873675.1	s__Lentibacillus litoralis	76.8592	91	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.836	128	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129485.1	s__Ornithinibacillus halophilus	76.7402	115	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628505.1	s__Oceanobacillus halophilus	76.6037	101	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000709085.1	s__Virgibacillus_B alimentarius	76.6004	119	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_B	95.0	99.59	99.59	0.92	0.92	2	-
GCF_002224365.1	s__Virgibacillus_F necropolis	76.5821	86	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	76.5555	98	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_001368815.1	s__Paraliobacillus sp001368815	76.531	75	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018916875.1	s__Virgibacillus proomii_B	76.4481	78	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	76.4183	96	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	76.3841	78	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	76.0448	78	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	75.7828	52	1006	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:21,175] [INFO] GTDB search result was written to GCF_008039555.1_ASM803955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:21,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:21,179] [INFO] DFAST_QC result json was written to GCF_008039555.1_ASM803955v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:21,180] [INFO] DFAST_QC completed!
[2024-01-24 11:28:21,180] [INFO] Total running time: 0h1m2s