[2024-01-24 13:40:28,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference
[2024-01-24 13:40:30,191] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:30,192] [INFO] Task started: Prodigal
[2024-01-24 13:40:30,192] [INFO] Running command: gunzip -c /var/lib/cwl/stgc10a1e0b-269a-448a-b884-13fcd699de4e/GCF_006539985.1_ASM653998v1_genomic.fna.gz | prodigal -d GCF_006539985.1_ASM653998v1_genomic.fna/cds.fna -a GCF_006539985.1_ASM653998v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:35,904] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:35,905] [INFO] Task started: HMMsearch
[2024-01-24 13:40:35,905] [INFO] Running command: hmmsearch --tblout GCF_006539985.1_ASM653998v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/reference_markers.hmm GCF_006539985.1_ASM653998v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:36,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:36,140] [INFO] Found 6/6 markers.
[2024-01-24 13:40:36,166] [INFO] Query marker FASTA was written to GCF_006539985.1_ASM653998v1_genomic.fna/markers.fasta
[2024-01-24 13:40:36,167] [INFO] Task started: Blastn
[2024-01-24 13:40:36,167] [INFO] Running command: blastn -query GCF_006539985.1_ASM653998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/reference_markers.fasta -out GCF_006539985.1_ASM653998v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:36,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:36,799] [INFO] Selected 13 target genomes.
[2024-01-24 13:40:36,799] [INFO] Target genome list was writen to GCF_006539985.1_ASM653998v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:36,806] [INFO] Task started: fastANI
[2024-01-24 13:40:36,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10a1e0b-269a-448a-b884-13fcd699de4e/GCF_006539985.1_ASM653998v1_genomic.fna.gz --refList GCF_006539985.1_ASM653998v1_genomic.fna/target_genomes.txt --output GCF_006539985.1_ASM653998v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:45,755] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:45,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:45,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:45,766] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:45,766] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:45,766] [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
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	99.9999	863	867	95	conclusive
Kurthia zopfii	strain=NCTC10597	GCA_900452285.1	1650	1650	type	True	80.4415	424	867	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	80.3522	423	867	95	below_threshold
Kurthia zopfii	strain=DSM 20580	GCA_004363595.1	1650	1650	type	True	80.3441	423	867	95	below_threshold
Kurthia zopfii	strain=NBRC 101529	GCA_007989745.1	1650	1650	type	True	80.2148	414	867	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.8043	134	867	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.5074	138	867	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.4369	126	867	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	76.9638	74	867	95	below_threshold
Paenisporosarcina antarctica	strain=CGMCC 1.6503	GCA_004367585.1	417367	417367	type	True	76.9448	68	867	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.5985	67	867	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.5932	71	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:45,773] [INFO] DFAST Taxonomy check result was written to GCF_006539985.1_ASM653998v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:45,774] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:45,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:45,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/checkm_data
[2024-01-24 13:40:45,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:45,804] [INFO] Task started: CheckM
[2024-01-24 13:40:45,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539985.1_ASM653998v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539985.1_ASM653998v1_genomic.fna/checkm_input GCF_006539985.1_ASM653998v1_genomic.fna/checkm_result
[2024-01-24 13:41:09,832] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:09,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,865] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:09,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:09,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539985.1_ASM653998v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:09,866] [INFO] Task started: Blastn
[2024-01-24 13:41:09,866] [INFO] Running command: blastn -query GCF_006539985.1_ASM653998v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28a8e797-4958-46a4-9ba2-ab52d30e1bb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539985.1_ASM653998v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:10,704] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:10,707] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:10,707] [INFO] Target genome list was writen to GCF_006539985.1_ASM653998v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:10,719] [INFO] Task started: fastANI
[2024-01-24 13:41:10,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10a1e0b-269a-448a-b884-13fcd699de4e/GCF_006539985.1_ASM653998v1_genomic.fna.gz --refList GCF_006539985.1_ASM653998v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539985.1_ASM653998v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:23,391] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:23,407] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:23,407] [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_006539985.1	s__Kurthia gibsonii	99.9999	863	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	97.46	97.18	0.93	0.90	4	conclusive
GCF_003143955.1	s__Kurthia zopfii	80.3386	424	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	99.54	98.21	0.97	0.90	5	-
GCA_018065935.1	s__Kurthia sp018065935	79.5427	313	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143975.1	s__Kurthia sibirica	78.9797	320	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000285555.1	s__Kurthia massiliensis	78.9183	248	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000285595.1	s__Kurthia senegalensis	78.8806	217	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003991225.1	s__Kurthia intestinigallinarum	78.5752	240	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Kurthia	95.0	98.65	98.48	0.94	0.89	8	-
GCF_002884495.1	s__Rummeliibacillus pycnus	78.0714	216	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	78.0295	156	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
GCF_002813185.1	s__Viridibacillus sp002813185	77.9189	197	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	98.00	98.00	0.85	0.85	2	-
GCF_003576525.1	s__Rummeliibacillus sp003576525	77.8482	202	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.66	98.66	0.89	0.89	2	-
GCF_001439635.1	s__Solibacillus cecembensis	77.8043	134	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Solibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274945.1	s__Viridibacillus arvi	77.6865	193	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	95.96	95.96	0.91	0.91	2	-
GCF_016908465.1	s__Ureibacillus composti	77.5345	127	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003966145.1	s__Ureibacillus telephonicus	77.3872	120	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628435.1	s__Ureibacillus endophyticus	77.3217	134	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Ureibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411295.1	s__Paenisporosarcina sp000411295	77.2661	78	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004367585.1	s__Paenisporosarcina antarctica	76.9448	68	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	95.47	95.47	0.86	0.86	2	-
GCF_000286315.1	s__Paenisporosarcina sp000286315	76.6105	68	867	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:23,409] [INFO] GTDB search result was written to GCF_006539985.1_ASM653998v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:23,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:23,414] [INFO] DFAST_QC result json was written to GCF_006539985.1_ASM653998v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:23,414] [INFO] DFAST_QC completed!
[2024-01-24 13:41:23,414] [INFO] Total running time: 0h0m55s