[2024-01-24 11:12:17,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:17,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:17,794] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference
[2024-01-24 11:12:18,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:18,956] [INFO] Task started: Prodigal
[2024-01-24 11:12:18,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgfde98859-54bb-4f86-9f97-ec94899d788b/GCF_027186265.1_ASM2718626v1_genomic.fna.gz | prodigal -d GCF_027186265.1_ASM2718626v1_genomic.fna/cds.fna -a GCF_027186265.1_ASM2718626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:28,273] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:28,274] [INFO] Task started: HMMsearch
[2024-01-24 11:12:28,274] [INFO] Running command: hmmsearch --tblout GCF_027186265.1_ASM2718626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/reference_markers.hmm GCF_027186265.1_ASM2718626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:28,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:28,549] [INFO] Found 6/6 markers.
[2024-01-24 11:12:28,583] [INFO] Query marker FASTA was written to GCF_027186265.1_ASM2718626v1_genomic.fna/markers.fasta
[2024-01-24 11:12:28,584] [INFO] Task started: Blastn
[2024-01-24 11:12:28,584] [INFO] Running command: blastn -query GCF_027186265.1_ASM2718626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/reference_markers.fasta -out GCF_027186265.1_ASM2718626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:29,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:29,190] [INFO] Selected 29 target genomes.
[2024-01-24 11:12:29,190] [INFO] Target genome list was writen to GCF_027186265.1_ASM2718626v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:31,867] [INFO] Task started: fastANI
[2024-01-24 11:12:31,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde98859-54bb-4f86-9f97-ec94899d788b/GCF_027186265.1_ASM2718626v1_genomic.fna.gz --refList GCF_027186265.1_ASM2718626v1_genomic.fna/target_genomes.txt --output GCF_027186265.1_ASM2718626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:48,220] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:48,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:48,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:48,299] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:12:48,299] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:12:48,299] [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
Sediminibacillus dalangtanensis	strain=DP4-553-S	GCA_017792025.1	2729421	2729421	type	True	78.8965	68	1250	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	78.6963	383	1250	95	below_threshold
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	78.1991	107	1250	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_018075365.1	1473	1473	type	True	78.0729	111	1250	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.3896	102	1250	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.3677	166	1250	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	77.3107	91	1250	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.1944	111	1250	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.1212	85	1250	95	below_threshold
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	77.0974	78	1250	95	below_threshold
Virgibacillus halodenitrificans	strain=JCM 12304	GCA_001310895.1	1482	1482	type	True	77.0819	92	1250	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	76.9575	103	1250	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.9374	93	1250	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_900156795.1	1473	1473	type	True	76.8861	102	1250	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	76.8811	109	1250	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	76.6148	102	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:48,301] [INFO] DFAST Taxonomy check result was written to GCF_027186265.1_ASM2718626v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:48,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:48,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:48,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/checkm_data
[2024-01-24 11:12:48,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:48,345] [INFO] Task started: CheckM
[2024-01-24 11:12:48,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027186265.1_ASM2718626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027186265.1_ASM2718626v1_genomic.fna/checkm_input GCF_027186265.1_ASM2718626v1_genomic.fna/checkm_result
[2024-01-24 11:13:23,958] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:23,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,982] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:23,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:23,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027186265.1_ASM2718626v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:23,985] [INFO] Task started: Blastn
[2024-01-24 11:13:23,985] [INFO] Running command: blastn -query GCF_027186265.1_ASM2718626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d843d7c-dcaf-4f84-b34f-a9fbd75d84cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_027186265.1_ASM2718626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:25,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:25,189] [INFO] Selected 28 target genomes.
[2024-01-24 11:13:25,190] [INFO] Target genome list was writen to GCF_027186265.1_ASM2718626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:25,524] [INFO] Task started: fastANI
[2024-01-24 11:13:25,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde98859-54bb-4f86-9f97-ec94899d788b/GCF_027186265.1_ASM2718626v1_genomic.fna.gz --refList GCF_027186265.1_ASM2718626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027186265.1_ASM2718626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:43,268] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:43,311] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:13:43,312] [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_009741735.1	s__Lentibacillus_B sp009741735	79.0932	65	1250	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	-
GCF_017792025.1	s__Sediminibacillus sp017792025	78.9329	66	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Sediminibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224365.1	s__Virgibacillus_F necropolis	78.5138	116	1250	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_000725285.1	s__Virgibacillus sp000725285	78.5075	97	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014642895.1	s__Virgibacillus_E populi	78.4777	380	1250	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_902806455.1	s__Lentibacillus doumboii	78.3895	138	1250	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_018075365.1	s__Virgibacillus pantothenticus	78.3124	111	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.44	97.53	0.92	0.86	18	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	78.1786	266	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373365.1	s__Lentibacillus sp013373365	78.0254	106	1250	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_001659985.1	s__Oceanobacillus sp001659985	77.6265	88	1250	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_900110695.1	s__Lentibacillus subterraneus	77.4268	100	1250	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_900129485.1	s__Ornithinibacillus halophilus	77.4091	88	1250	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_003369565.1	s__Oceanobacillus chungangensis	77.3715	89	1250	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_014638995.1	s__Virgibacillus_E oceani	77.3677	166	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873675.1	s__Lentibacillus litoralis	77.2166	110	1250	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_900112705.1	s__Lentibacillus persicus	77.186	78	1250	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_010994035.1	s__Virgibacillus sp010994035	77.167	88	1250	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_003730295.1	s__LJ137 sp003730295	77.1212	85	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310895.1	s__Virgibacillus halodenitrificans	77.0793	93	1250	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_009733865.1	s__Oceanobacillus salinisoli	76.9655	92	1250	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_008304605.1	s__Oceanobacillus polygoni	76.8868	108	1250	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:43,314] [INFO] GTDB search result was written to GCF_027186265.1_ASM2718626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:43,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:43,319] [INFO] DFAST_QC result json was written to GCF_027186265.1_ASM2718626v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:43,319] [INFO] DFAST_QC completed!
[2024-01-24 11:13:43,319] [INFO] Total running time: 0h1m26s