[2024-01-25 18:13:05,579] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference
[2024-01-25 18:13:06,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:06,686] [INFO] Task started: Prodigal
[2024-01-25 18:13:06,686] [INFO] Running command: gunzip -c /var/lib/cwl/stge0b3588c-edd3-4268-9f1d-5d9aed96ca64/GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna.gz | prodigal -d GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/cds.fna -a GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:11,849] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:11,849] [INFO] Task started: HMMsearch
[2024-01-25 18:13:11,849] [INFO] Running command: hmmsearch --tblout GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/reference_markers.hmm GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:12,067] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:12,068] [INFO] Found 6/6 markers.
[2024-01-25 18:13:12,096] [INFO] Query marker FASTA was written to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/markers.fasta
[2024-01-25 18:13:12,096] [INFO] Task started: Blastn
[2024-01-25 18:13:12,096] [INFO] Running command: blastn -query GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/reference_markers.fasta -out GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:12,648] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:12,651] [INFO] Selected 24 target genomes.
[2024-01-25 18:13:12,651] [INFO] Target genome list was writen to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/target_genomes.txt
[2024-01-25 18:13:12,670] [INFO] Task started: fastANI
[2024-01-25 18:13:12,671] [INFO] Running command: fastANI --query /var/lib/cwl/stge0b3588c-edd3-4268-9f1d-5d9aed96ca64/GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna.gz --refList GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/target_genomes.txt --output GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:26,728] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:26,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:26,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:26,738] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:13:26,738] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:26,739] [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
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	100.0	933	943	95	conclusive
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.1948	92	943	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.116	130	943	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	76.9672	84	943	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	76.8443	87	943	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.7891	106	943	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_000723585.1	1462526	1462526	suspected-type	True	76.786	116	943	95	below_threshold
Radiobacillus deserti	strain=TKL69	GCA_007301515.1	2594883	2594883	type	True	76.7452	50	943	95	below_threshold
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	76.694	108	943	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	76.6687	75	943	95	below_threshold
Virgibacillus massiliensis	strain=Vm-5	GCA_014905475.1	1462526	1462526	suspected-type	True	76.6447	119	943	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	76.6337	82	943	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.6304	125	943	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.6096	109	943	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.3155	61	943	95	below_threshold
Aquibacillus saliphilus	strain=KHM2	GCA_020404745.1	1909422	1909422	type	True	76.2153	63	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:26,740] [INFO] DFAST Taxonomy check result was written to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/tc_result.tsv
[2024-01-25 18:13:26,740] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:26,741] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:26,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/checkm_data
[2024-01-25 18:13:26,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:26,773] [INFO] Task started: CheckM
[2024-01-25 18:13:26,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/checkm_input GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/checkm_result
[2024-01-25 18:13:47,562] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:47,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:47,589] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:47,589] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:47,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/markers.fasta)
[2024-01-25 18:13:47,590] [INFO] Task started: Blastn
[2024-01-25 18:13:47,590] [INFO] Running command: blastn -query GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc2716b1-42fa-4762-a5d2-2aa2bf95c7d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:48,388] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:48,391] [INFO] Selected 27 target genomes.
[2024-01-25 18:13:48,391] [INFO] Target genome list was writen to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:48,432] [INFO] Task started: fastANI
[2024-01-25 18:13:48,432] [INFO] Running command: fastANI --query /var/lib/cwl/stge0b3588c-edd3-4268-9f1d-5d9aed96ca64/GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna.gz --refList GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/target_genomes_gtdb.txt --output GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:04,851] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:04,860] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:04,861] [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_000709085.1	s__Virgibacillus_B alimentarius	100.0	933	943	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	conclusive
GCF_002266285.1	s__Virgibacillus_G indicus	77.116	130	943	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_001368815.1	s__Paraliobacillus sp001368815	77.0347	56	943	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_003369565.1	s__Oceanobacillus chungangensis	76.9672	84	943	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_900166595.1	s__Virgibacillus dokdonensis	76.9138	94	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.5968	98.95	98.88	0.93	0.90	3	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.9118	130	943	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_000725285.1	s__Virgibacillus sp000725285	76.8094	121	943	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_900129485.1	s__Ornithinibacillus halophilus	76.7891	106	943	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_900258515.1	s__Virgibacillus_E sp900258515	76.7486	151	943	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_014905415.1	s__Virgibacillus salexigens	76.7078	117	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.53	99.42	0.93	0.91	9	-
GCF_008039555.1	s__Cerasibacillus terrae	76.694	108	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	99.05	99.05	0.92	0.92	2	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.6722	138	943	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_900111445.1	s__Ornithinibacillus limi	76.6291	109	943	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_001307805.1	s__Lentibacillus amyloliquefaciens	76.6289	81	943	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_900176885.1	s__Oceanobacillus senegalensis	76.6096	109	943	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:04,862] [INFO] GTDB search result was written to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:04,863] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:04,866] [INFO] DFAST_QC result json was written to GCF_000709085.1_Virgibacillus_alimentarius_J18_genomic.fna/dqc_result.json
[2024-01-25 18:14:04,866] [INFO] DFAST_QC completed!
[2024-01-25 18:14:04,866] [INFO] Total running time: 0h0m59s