[2024-01-24 13:41:26,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference
[2024-01-24 13:41:28,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:28,012] [INFO] Task started: Prodigal
[2024-01-24 13:41:28,012] [INFO] Running command: gunzip -c /var/lib/cwl/stg461f73d2-10a9-434f-b101-9f6f18784679/GCF_002153375.1_ASM215337v1_genomic.fna.gz | prodigal -d GCF_002153375.1_ASM215337v1_genomic.fna/cds.fna -a GCF_002153375.1_ASM215337v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:36,624] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:36,625] [INFO] Task started: HMMsearch
[2024-01-24 13:41:36,625] [INFO] Running command: hmmsearch --tblout GCF_002153375.1_ASM215337v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/reference_markers.hmm GCF_002153375.1_ASM215337v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:36,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:36,924] [INFO] Found 6/6 markers.
[2024-01-24 13:41:36,958] [INFO] Query marker FASTA was written to GCF_002153375.1_ASM215337v1_genomic.fna/markers.fasta
[2024-01-24 13:41:36,959] [INFO] Task started: Blastn
[2024-01-24 13:41:36,959] [INFO] Running command: blastn -query GCF_002153375.1_ASM215337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/reference_markers.fasta -out GCF_002153375.1_ASM215337v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:37,590] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:37,608] [INFO] Selected 24 target genomes.
[2024-01-24 13:41:37,609] [INFO] Target genome list was writen to GCF_002153375.1_ASM215337v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:37,625] [INFO] Task started: fastANI
[2024-01-24 13:41:37,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg461f73d2-10a9-434f-b101-9f6f18784679/GCF_002153375.1_ASM215337v1_genomic.fna.gz --refList GCF_002153375.1_ASM215337v1_genomic.fna/target_genomes.txt --output GCF_002153375.1_ASM215337v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:54,103] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:54,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:54,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:54,125] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:54,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:54,125] [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 rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	100.0	1283	1283	95	conclusive
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	79.5078	506	1283	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	78.7241	326	1283	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.6428	356	1283	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	78.6419	330	1283	95	below_threshold
Oceanobacillus massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	78.4891	344	1283	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.6685	237	1283	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.6594	252	1283	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.6363	213	1283	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.5505	125	1283	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	77.368	182	1283	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.2514	189	1283	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.2108	169	1283	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	77.0269	136	1283	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	76.9637	131	1283	95	below_threshold
Gracilibacillus kekensis	strain=CGMCC 1.10681	GCA_900143085.1	1027249	1027249	type	True	76.8559	73	1283	95	below_threshold
Lentibacillus saliphilus	strain=YIM 93176	GCA_019093865.1	2737028	2737028	type	True	76.5351	68	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:54,127] [INFO] DFAST Taxonomy check result was written to GCF_002153375.1_ASM215337v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:54,127] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:54,128] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:54,128] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/checkm_data
[2024-01-24 13:41:54,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:54,168] [INFO] Task started: CheckM
[2024-01-24 13:41:54,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002153375.1_ASM215337v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002153375.1_ASM215337v1_genomic.fna/checkm_input GCF_002153375.1_ASM215337v1_genomic.fna/checkm_result
[2024-01-24 13:42:24,480] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:24,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,503] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:24,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:24,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002153375.1_ASM215337v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:24,505] [INFO] Task started: Blastn
[2024-01-24 13:42:24,505] [INFO] Running command: blastn -query GCF_002153375.1_ASM215337v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf3ec126-78cb-452b-922f-a426a991e5a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002153375.1_ASM215337v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:25,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:25,283] [INFO] Selected 20 target genomes.
[2024-01-24 13:42:25,283] [INFO] Target genome list was writen to GCF_002153375.1_ASM215337v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:25,301] [INFO] Task started: fastANI
[2024-01-24 13:42:25,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg461f73d2-10a9-434f-b101-9f6f18784679/GCF_002153375.1_ASM215337v1_genomic.fna.gz --refList GCF_002153375.1_ASM215337v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002153375.1_ASM215337v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:38,934] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:38,953] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:38,953] [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_002153375.1	s__Oceanobacillus rekensis	100.0	1283	1283	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_001618145.1	s__Oceanobacillus damuensis	79.4846	509	1283	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_003515705.1	s__Oceanobacillus profundus	78.7045	327	1283	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_008304605.1	s__Oceanobacillus polygoni	78.6488	358	1283	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_000285495.1	s__Oceanobacillus massiliensis	78.4843	345	1283	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_002266285.1	s__Virgibacillus_G indicus	77.6566	213	1283	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_003369575.1	s__Oceanobacillus arenosus	77.651	239	1283	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_002287375.1	s__Virgibacillus_G profundi	77.6497	255	1283	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_001310895.1	s__Virgibacillus halodenitrificans	77.5698	126	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	98.29	98.21	0.89	0.88	7	-
GCF_000340475.1	s__Oceanobacillus kimchii	77.3675	182	1283	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_003628445.1	s__Oceanobacillus bengalensis	77.267	188	1283	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_016908515.1	s__Virgibacillus_I halotolerans	77.2108	169	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645515.1	s__Oceanobacillus neutriphilus	77.04	137	1283	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_900143085.1	s__Gracilibacillus kekensis	76.8559	73	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	76.789	138	1283	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_900184735.1	s__Ornithinibacillus globulus_B	76.7236	115	1283	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_019093865.1	s__Lentibacillus_B saliphilus	76.5351	68	1283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:38,955] [INFO] GTDB search result was written to GCF_002153375.1_ASM215337v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:38,956] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:38,962] [INFO] DFAST_QC result json was written to GCF_002153375.1_ASM215337v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:38,962] [INFO] DFAST_QC completed!
[2024-01-24 13:42:38,962] [INFO] Total running time: 0h1m12s