[2024-01-24 14:47:21,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:21,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:21,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference
[2024-01-24 14:47:25,109] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:25,110] [INFO] Task started: Prodigal
[2024-01-24 14:47:25,110] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c6d956a-1356-455d-972d-ca08cf9c351a/GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/cds.fna -a GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:33,614] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:33,614] [INFO] Task started: HMMsearch
[2024-01-24 14:47:33,615] [INFO] Running command: hmmsearch --tblout GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/reference_markers.hmm GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:34,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:34,041] [INFO] Found 6/6 markers.
[2024-01-24 14:47:34,083] [INFO] Query marker FASTA was written to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:34,084] [INFO] Task started: Blastn
[2024-01-24 14:47:34,084] [INFO] Running command: blastn -query GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/reference_markers.fasta -out GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:34,872] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:34,875] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:34,875] [INFO] Target genome list was writen to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:34,985] [INFO] Task started: fastANI
[2024-01-24 14:47:34,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c6d956a-1356-455d-972d-ca08cf9c351a/GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna.gz --refList GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:53,005] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:53,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:53,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:53,023] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:53,023] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:53,023] [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
Gracilibacillus kekensis	strain=CGMCC 1.10681	GCA_900143085.1	1027249	1027249	type	True	100.0	1318	1319	95	conclusive
Gracilibacillus massiliensis	strain=Awa-1	GCA_001458115.1	1564956	1564956	type	True	88.2465	1044	1319	95	below_threshold
Gracilibacillus boraciitolerans	strain=JCM 21714	GCA_000521485.1	307521	307521	type	True	79.4878	556	1319	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	79.3117	512	1319	95	below_threshold
Gracilibacillus lacisalsi	strain=DSM 19029	GCA_000377765.1	393087	393087	type	True	79.0744	459	1319	95	below_threshold
Gracilibacillus saliphilus	strain=YIM 91119	GCA_010994085.1	543890	543890	type	True	79.0586	465	1319	95	below_threshold
Gracilibacillus orientalis	strain=CGMCC 1.4250	GCA_900114645.1	334253	334253	type	True	78.8015	471	1319	95	below_threshold
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	77.0868	60	1319	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.0153	75	1319	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	76.7751	80	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:53,024] [INFO] DFAST Taxonomy check result was written to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:47:53,025] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:53,025] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:53,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/checkm_data
[2024-01-24 14:47:53,026] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:53,069] [INFO] Task started: CheckM
[2024-01-24 14:47:53,069] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/checkm_input GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:48:22,525] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:22,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:22,542] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:22,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:22,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:48:22,543] [INFO] Task started: Blastn
[2024-01-24 14:48:22,543] [INFO] Running command: blastn -query GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4bc8f735-306b-4856-a923-357f95658929/dqc_reference/reference_markers_gtdb.fasta -out GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:23,438] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:23,444] [INFO] Selected 17 target genomes.
[2024-01-24 14:48:23,444] [INFO] Target genome list was writen to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:23,457] [INFO] Task started: fastANI
[2024-01-24 14:48:23,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c6d956a-1356-455d-972d-ca08cf9c351a/GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna.gz --refList GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:37,682] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:37,699] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:37,700] [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_900143085.1	s__Gracilibacillus kekensis	100.0	1318	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001458115.1	s__Gracilibacillus massiliensis	88.2229	1046	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000521485.1	s__Gracilibacillus boraciitolerans	79.4926	555	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650095.1	s__Gracilibacillus sp002797295	79.3359	510	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_000377765.1	s__Gracilibacillus lacisalsi	79.0786	459	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	95.88	95.36	0.83	0.81	4	-
GCF_900114645.1	s__Gracilibacillus orientalis	78.8109	470	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993965.1	s__Gracilibacillus sp010993965	77.4794	226	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266285.1	s__Virgibacillus_G indicus	77.1167	55	1319	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_900103695.1	s__Sediminibacillus halophilus	77.0484	59	1319	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_003352005.1	s__Oceanobacillus zhaokaii	77.0115	75	1319	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_003426025.1	s__Paraliobacillus_A quinghaiensis	76.8582	117	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002153375.1	s__Oceanobacillus rekensis	76.855	70	1319	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_003268595.1	s__Paraliobacillus_A zengyii	76.7795	123	1319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_900176885.1	s__Oceanobacillus senegalensis	76.7518	79	1319	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 14:48:37,701] [INFO] GTDB search result was written to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:37,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:37,705] [INFO] DFAST_QC result json was written to GCF_900143085.1_IMG-taxon_2667528169_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:48:37,705] [INFO] DFAST_QC completed!
[2024-01-24 14:48:37,705] [INFO] Total running time: 0h1m16s