[2024-01-24 14:54:49,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference
[2024-01-24 14:54:50,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,497] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,497] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb6a3c79-df6c-43b5-8f87-fbd7887ced28/GCF_004367585.1_ASM436758v1_genomic.fna.gz | prodigal -d GCF_004367585.1_ASM436758v1_genomic.fna/cds.fna -a GCF_004367585.1_ASM436758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:58,773] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:58,774] [INFO] Task started: HMMsearch
[2024-01-24 14:54:58,774] [INFO] Running command: hmmsearch --tblout GCF_004367585.1_ASM436758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/reference_markers.hmm GCF_004367585.1_ASM436758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:59,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:59,053] [INFO] Found 6/6 markers.
[2024-01-24 14:54:59,089] [INFO] Query marker FASTA was written to GCF_004367585.1_ASM436758v1_genomic.fna/markers.fasta
[2024-01-24 14:54:59,089] [INFO] Task started: Blastn
[2024-01-24 14:54:59,089] [INFO] Running command: blastn -query GCF_004367585.1_ASM436758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/reference_markers.fasta -out GCF_004367585.1_ASM436758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:59,696] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:59,700] [INFO] Selected 21 target genomes.
[2024-01-24 14:54:59,700] [INFO] Target genome list was writen to GCF_004367585.1_ASM436758v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:59,737] [INFO] Task started: fastANI
[2024-01-24 14:54:59,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb6a3c79-df6c-43b5-8f87-fbd7887ced28/GCF_004367585.1_ASM436758v1_genomic.fna.gz --refList GCF_004367585.1_ASM436758v1_genomic.fna/target_genomes.txt --output GCF_004367585.1_ASM436758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:14,291] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:14,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:14,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:14,311] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:14,311] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:14,312] [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
Paenisporosarcina antarctica	strain=CGMCC 1.6503	GCA_004367585.1	417367	417367	type	True	100.0	1323	1324	95	conclusive
Paenisporosarcina cavernae	strain=K2R23-3	GCA_003595195.1	2320858	2320858	type	True	79.7356	144	1324	95	below_threshold
Paenisporosarcina indica	strain=PN2	GCA_001939075.1	650093	650093	type	True	79.6793	440	1324	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	79.5101	74	1324	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	79.3898	66	1324	95	below_threshold
Metabacillus halosaccharovorans	strain=DSM 25387	GCA_002019635.1	930124	930124	type	True	79.2022	75	1324	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	78.2442	166	1324	95	below_threshold
Viridibacillus soli	strain=YIM B01967	GCA_016612995.1	2798301	2798301	type	True	77.8671	110	1324	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	77.7464	140	1324	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	77.6648	151	1324	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	77.5354	153	1324	95	below_threshold
Viridibacillus arvi	strain=DSM 16317	GCA_001274945.1	263475	263475	type	True	77.472	123	1324	95	below_threshold
Lysinibacillus capsici	strain=PB300	GCA_003367505.1	2115968	2115968	type	True	77.4192	102	1324	95	below_threshold
Solibacillus isronensis	strain=B3W22	GCA_000298255.1	412383	412383	type	True	77.3595	77	1324	95	below_threshold
Kurthia zopfii	strain=ATCC 33403	GCA_003143955.1	1650	1650	type	True	77.3002	74	1324	95	below_threshold
Ureibacillus chungkukjangi	strain=KACC 16626	GCA_003217295.1	1202712	1202712	type	True	77.2312	92	1324	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	77.1845	95	1324	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.1009	103	1324	95	below_threshold
Kurthia gibsonii	strain=NBRC 15534	GCA_006539985.1	33946	33946	type	True	76.9642	75	1324	95	below_threshold
Filibacter tadaridae		GCA_900609045.1	2483811	2483811	type	True	76.7791	68	1324	95	below_threshold
Litchfieldia salsa	strain=IBRC-M10078	GCA_900104555.1	930152	930152	type	True	76.5178	65	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:14,313] [INFO] DFAST Taxonomy check result was written to GCF_004367585.1_ASM436758v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:14,314] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:14,314] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:14,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/checkm_data
[2024-01-24 14:55:14,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:14,353] [INFO] Task started: CheckM
[2024-01-24 14:55:14,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004367585.1_ASM436758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004367585.1_ASM436758v1_genomic.fna/checkm_input GCF_004367585.1_ASM436758v1_genomic.fna/checkm_result
[2024-01-24 14:55:44,294] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:44,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:44,314] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:44,314] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:44,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004367585.1_ASM436758v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:44,315] [INFO] Task started: Blastn
[2024-01-24 14:55:44,315] [INFO] Running command: blastn -query GCF_004367585.1_ASM436758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg796ae7e6-0bab-4827-879c-816c6e9c20ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_004367585.1_ASM436758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:45,075] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:45,080] [INFO] Selected 8 target genomes.
[2024-01-24 14:55:45,080] [INFO] Target genome list was writen to GCF_004367585.1_ASM436758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:45,092] [INFO] Task started: fastANI
[2024-01-24 14:55:45,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb6a3c79-df6c-43b5-8f87-fbd7887ced28/GCF_004367585.1_ASM436758v1_genomic.fna.gz --refList GCF_004367585.1_ASM436758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004367585.1_ASM436758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:52,646] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:52,654] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:52,654] [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_004367585.1	s__Paenisporosarcina antarctica	100.0	1323	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	95.47	95.47	0.86	0.86	2	conclusive
GCF_000286315.1	s__Paenisporosarcina sp000286315	81.8894	679	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000484595.1	s__Paenisporosarcina sp000484595	81.8198	684	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058165.1	s__Paenisporosarcina sp003058165	81.6798	690	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411295.1	s__Paenisporosarcina sp000411295	80.3932	512	1324	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_001939075.1	s__Paenisporosarcina indica	79.6774	441	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Paenisporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274945.1	s__Viridibacillus arvi	77.5318	122	1324	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_001955655.1	s__Viridibacillus arenosi	77.1608	140	1324	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Viridibacillus	95.0	99.71	99.53	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:52,655] [INFO] GTDB search result was written to GCF_004367585.1_ASM436758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:52,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:52,659] [INFO] DFAST_QC result json was written to GCF_004367585.1_ASM436758v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:52,660] [INFO] DFAST_QC completed!
[2024-01-24 14:55:52,660] [INFO] Total running time: 0h1m3s