[2024-01-24 13:58:10,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,506] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference
[2024-01-24 13:58:11,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,585] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,585] [INFO] Running command: gunzip -c /var/lib/cwl/stgea3b17dd-b8ab-4cfd-8a0b-d61d4c8aacb0/GCF_001618145.1_ASM161814v1_genomic.fna.gz | prodigal -d GCF_001618145.1_ASM161814v1_genomic.fna/cds.fna -a GCF_001618145.1_ASM161814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:19,615] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:19,616] [INFO] Task started: HMMsearch
[2024-01-24 13:58:19,616] [INFO] Running command: hmmsearch --tblout GCF_001618145.1_ASM161814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/reference_markers.hmm GCF_001618145.1_ASM161814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:19,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:19,850] [INFO] Found 6/6 markers.
[2024-01-24 13:58:19,879] [INFO] Query marker FASTA was written to GCF_001618145.1_ASM161814v1_genomic.fna/markers.fasta
[2024-01-24 13:58:19,880] [INFO] Task started: Blastn
[2024-01-24 13:58:19,880] [INFO] Running command: blastn -query GCF_001618145.1_ASM161814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/reference_markers.fasta -out GCF_001618145.1_ASM161814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:20,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:20,441] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:20,441] [INFO] Target genome list was writen to GCF_001618145.1_ASM161814v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:20,511] [INFO] Task started: fastANI
[2024-01-24 13:58:20,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgea3b17dd-b8ab-4cfd-8a0b-d61d4c8aacb0/GCF_001618145.1_ASM161814v1_genomic.fna.gz --refList GCF_001618145.1_ASM161814v1_genomic.fna/target_genomes.txt --output GCF_001618145.1_ASM161814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:35,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:35,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:35,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:35,619] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:35,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:35,619] [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
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	100.0	1334	1338	95	conclusive
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	79.548	507	1338	95	below_threshold
Oceanobacillus massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	79.0609	374	1338	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.7271	335	1338	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	78.4901	317	1338	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	78.4873	318	1338	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.3795	182	1338	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	78.0918	182	1338	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.8298	169	1338	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.6904	190	1338	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.6696	134	1338	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.4827	197	1338	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.4386	94	1338	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	76.9213	155	1338	95	below_threshold
Aquibacillus sediminis	strain=BH258	GCA_005870085.1	2574734	2574734	type	True	76.8334	66	1338	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.7558	89	1338	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	76.7036	51	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:35,623] [INFO] DFAST Taxonomy check result was written to GCF_001618145.1_ASM161814v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:35,624] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:35,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:35,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/checkm_data
[2024-01-24 13:58:35,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:35,665] [INFO] Task started: CheckM
[2024-01-24 13:58:35,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001618145.1_ASM161814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001618145.1_ASM161814v1_genomic.fna/checkm_input GCF_001618145.1_ASM161814v1_genomic.fna/checkm_result
[2024-01-24 13:59:02,974] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:02,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,990] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:02,990] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:02,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001618145.1_ASM161814v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:02,991] [INFO] Task started: Blastn
[2024-01-24 13:59:02,991] [INFO] Running command: blastn -query GCF_001618145.1_ASM161814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e6ec95a-c4f6-4fdc-8935-98f17e837987/dqc_reference/reference_markers_gtdb.fasta -out GCF_001618145.1_ASM161814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:03,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:03,743] [INFO] Selected 18 target genomes.
[2024-01-24 13:59:03,743] [INFO] Target genome list was writen to GCF_001618145.1_ASM161814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:03,752] [INFO] Task started: fastANI
[2024-01-24 13:59:03,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgea3b17dd-b8ab-4cfd-8a0b-d61d4c8aacb0/GCF_001618145.1_ASM161814v1_genomic.fna.gz --refList GCF_001618145.1_ASM161814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001618145.1_ASM161814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:17,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:17,273] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:17,273] [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_001618145.1	s__Oceanobacillus damuensis	100.0	1334	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002153375.1	s__Oceanobacillus rekensis	79.5582	506	1338	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_000285495.1	s__Oceanobacillus massiliensis	79.0609	374	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008304605.1	s__Oceanobacillus polygoni	78.7399	334	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003515705.1	s__Oceanobacillus profundus	78.4938	316	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_003352005.1	s__Oceanobacillus zhaokaii	78.3383	186	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_009733865.1	s__Oceanobacillus salinisoli	78.1294	183	1338	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_003369565.1	s__Oceanobacillus chungangensis	77.8908	166	1338	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_002266285.1	s__Virgibacillus_G indicus	77.7083	190	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340475.1	s__Oceanobacillus kimchii	77.6936	133	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_001038425.2	s__Ornithinibacillus contaminans	77.4982	94	1338	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_002287375.1	s__Virgibacillus_G profundi	77.4497	200	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016919725.1	s__Virgibacillus sp016919725	77.2578	107	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_000577245.1	s__Ornithinibacillus sp000577245	77.0385	110	1338	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_003628445.1	s__Oceanobacillus bengalensis	76.8938	157	1338	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_005870085.1	s__BH258 sp005870085	76.8334	66	1338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__BH258	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:17,275] [INFO] GTDB search result was written to GCF_001618145.1_ASM161814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:17,276] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:17,279] [INFO] DFAST_QC result json was written to GCF_001618145.1_ASM161814v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:17,279] [INFO] DFAST_QC completed!
[2024-01-24 13:59:17,279] [INFO] Total running time: 0h1m7s