[2024-01-24 14:22:03,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference
[2024-01-24 14:22:04,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:04,876] [INFO] Task started: Prodigal
[2024-01-24 14:22:04,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg271d4f4a-32f5-4508-b248-1f612b2822f4/GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/cds.fna -a GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:13,786] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:13,786] [INFO] Task started: HMMsearch
[2024-01-24 14:22:13,787] [INFO] Running command: hmmsearch --tblout GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/reference_markers.hmm GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:14,047] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:14,048] [INFO] Found 6/6 markers.
[2024-01-24 14:22:14,082] [INFO] Query marker FASTA was written to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:14,083] [INFO] Task started: Blastn
[2024-01-24 14:22:14,083] [INFO] Running command: blastn -query GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/reference_markers.fasta -out GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:14,696] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:14,710] [INFO] Selected 22 target genomes.
[2024-01-24 14:22:14,711] [INFO] Target genome list was writen to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:14,731] [INFO] Task started: fastANI
[2024-01-24 14:22:14,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg271d4f4a-32f5-4508-b248-1f612b2822f4/GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna.gz --refList GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:29,832] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:29,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:29,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:29,844] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:29,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:29,844] [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
Lentibacillus persicus	strain=DSM 22530	GCA_900112705.1	640948	640948	type	True	100.0	1094	1094	95	conclusive
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	81.4976	720	1094	95	below_threshold
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	78.5846	380	1094	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	78.0618	335	1094	95	below_threshold
Lentibacillus kapialis	strain=JCM 12580	GCA_014646635.1	340214	340214	type	True	77.7794	298	1094	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	77.6259	166	1094	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	77.1958	78	1094	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.9831	85	1094	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	76.9036	67	1094	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	76.8821	65	1094	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	76.8503	132	1094	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	76.7665	100	1094	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:29,846] [INFO] DFAST Taxonomy check result was written to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:22:29,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:29,847] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:29,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/checkm_data
[2024-01-24 14:22:29,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:29,887] [INFO] Task started: CheckM
[2024-01-24 14:22:29,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/checkm_input GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:23:00,785] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:00,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,809] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:00,809] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:00,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:23:00,810] [INFO] Task started: Blastn
[2024-01-24 14:23:00,810] [INFO] Running command: blastn -query GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bd9619b-db65-45fc-8f6a-cf746fb37b40/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:01,565] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:01,569] [INFO] Selected 19 target genomes.
[2024-01-24 14:23:01,569] [INFO] Target genome list was writen to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:01,586] [INFO] Task started: fastANI
[2024-01-24 14:23:01,586] [INFO] Running command: fastANI --query /var/lib/cwl/stg271d4f4a-32f5-4508-b248-1f612b2822f4/GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna.gz --refList GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:15,290] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:15,308] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:15,309] [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_900112705.1	s__Lentibacillus persicus	100.0	1094	1094	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001307805.1	s__Lentibacillus amyloliquefaciens	81.5014	719	1094	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_000224785.1	s__Lentibacillus jeotgali	78.6022	377	1094	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_013373365.1	s__Lentibacillus sp013373365	78.5601	449	1094	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_004565465.1	s__Lentibacillus salicampi	78.0868	318	1094	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_900112045.1	s__Lentibacillus halodurans	78.0815	333	1094	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_014646635.1	s__Lentibacillus kapialis	77.7906	297	1094	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_005887555.1	s__Lentibacillus cibarius	77.6317	167	1094	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	-
GCF_010993955.1	s__YIM-98839 sp010993955	77.0973	78	1094	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_902806455.1	s__Lentibacillus doumboii	77.0024	174	1094	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_900162615.1	s__Virgibacillus proomii_A	76.9722	62	1094	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_018916875.1	s__Virgibacillus proomii_B	76.97	59	1094	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_003515705.1	s__Oceanobacillus profundus	76.8792	66	1094	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_017873675.1	s__Lentibacillus litoralis	76.7991	134	1094	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_900258515.1	s__Virgibacillus_E sp900258515	76.6911	100	1094	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_900162665.1	s__Oceanobacillus sojae_A	76.6784	56	1094	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:15,311] [INFO] GTDB search result was written to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:15,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:15,317] [INFO] DFAST_QC result json was written to GCF_900112705.1_IMG-taxon_2651870107_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:23:15,318] [INFO] DFAST_QC completed!
[2024-01-24 14:23:15,318] [INFO] Total running time: 0h1m12s