[2024-01-24 13:13:12,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference
[2024-01-24 13:13:13,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,997] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,997] [INFO] Running command: gunzip -c /var/lib/cwl/stgf720dba9-2742-4897-a398-486c6338f7c0/GCF_003605405.2_ASM360540v2_genomic.fna.gz | prodigal -d GCF_003605405.2_ASM360540v2_genomic.fna/cds.fna -a GCF_003605405.2_ASM360540v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:27,042] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:27,043] [INFO] Task started: HMMsearch
[2024-01-24 13:13:27,043] [INFO] Running command: hmmsearch --tblout GCF_003605405.2_ASM360540v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/reference_markers.hmm GCF_003605405.2_ASM360540v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:27,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:27,411] [INFO] Found 6/6 markers.
[2024-01-24 13:13:27,457] [INFO] Query marker FASTA was written to GCF_003605405.2_ASM360540v2_genomic.fna/markers.fasta
[2024-01-24 13:13:27,457] [INFO] Task started: Blastn
[2024-01-24 13:13:27,457] [INFO] Running command: blastn -query GCF_003605405.2_ASM360540v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/reference_markers.fasta -out GCF_003605405.2_ASM360540v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:28,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:28,068] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:28,068] [INFO] Target genome list was writen to GCF_003605405.2_ASM360540v2_genomic.fna/target_genomes.txt
[2024-01-24 13:13:28,457] [INFO] Task started: fastANI
[2024-01-24 13:13:28,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgf720dba9-2742-4897-a398-486c6338f7c0/GCF_003605405.2_ASM360540v2_genomic.fna.gz --refList GCF_003605405.2_ASM360540v2_genomic.fna/target_genomes.txt --output GCF_003605405.2_ASM360540v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:47,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:47,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:47,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:47,714] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:47,714] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:47,714] [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
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	83.7217	855	1735	95	below_threshold
Siminovitchia fordii	strain=DSM 16014	GCA_000374565.1	254759	254759	type	True	83.4451	994	1735	95	below_threshold
Siminovitchia acidinfaciens	strain=3-2-2	GCA_003605385.2	2321395	2321395	type	True	80.6346	763	1735	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.8425	78	1735	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	77.7553	124	1735	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.6146	55	1735	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.1743	87	1735	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	77.1582	86	1735	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.8747	70	1735	95	below_threshold
Litchfieldia alkalitelluris	strain=DSM 16976	GCA_002019645.1	304268	304268	type	True	76.5498	55	1735	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.2799	53	1735	95	below_threshold
Bacillus thuringiensis	strain=ATCC 10792	GCA_002119445.1	1428	1428	suspected-type	True	76.2525	53	1735	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	76.0497	56	1735	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:47,716] [INFO] DFAST Taxonomy check result was written to GCF_003605405.2_ASM360540v2_genomic.fna/tc_result.tsv
[2024-01-24 13:13:47,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:47,717] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:47,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/checkm_data
[2024-01-24 13:13:47,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:47,773] [INFO] Task started: CheckM
[2024-01-24 13:13:47,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003605405.2_ASM360540v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003605405.2_ASM360540v2_genomic.fna/checkm_input GCF_003605405.2_ASM360540v2_genomic.fna/checkm_result
[2024-01-24 13:14:28,696] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:28,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:28,722] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:28,722] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:28,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003605405.2_ASM360540v2_genomic.fna/markers.fasta)
[2024-01-24 13:14:28,723] [INFO] Task started: Blastn
[2024-01-24 13:14:28,724] [INFO] Running command: blastn -query GCF_003605405.2_ASM360540v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcd21939-593e-4a97-8e6c-d6680728523b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003605405.2_ASM360540v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:29,460] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:29,463] [INFO] Selected 6 target genomes.
[2024-01-24 13:14:29,463] [INFO] Target genome list was writen to GCF_003605405.2_ASM360540v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:29,469] [INFO] Task started: fastANI
[2024-01-24 13:14:29,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgf720dba9-2742-4897-a398-486c6338f7c0/GCF_003605405.2_ASM360540v2_genomic.fna.gz --refList GCF_003605405.2_ASM360540v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003605405.2_ASM360540v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:42,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:42,079] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:42,079] [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_003605405.2	s__Siminovitchia terrae	100.0	1731	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	99.14	99.09	0.90	0.90	3	conclusive
GCF_009928435.1	s__Siminovitchia sp009928435	90.7409	985	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836955.1	s__Siminovitchia sp014836955	90.4762	1233	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605365.2	s__Siminovitchia fortis	83.7236	856	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.09	98.04	0.87	0.87	16	-
GCF_000374565.1	s__Siminovitchia fordii	83.303	1014	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	98.95	97.34	0.95	0.89	4	-
GCF_003605385.1	s__Siminovitchia acidinfaciens	80.6751	756	1735	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Siminovitchia	95.0	96.47	96.47	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:42,081] [INFO] GTDB search result was written to GCF_003605405.2_ASM360540v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:42,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:42,086] [INFO] DFAST_QC result json was written to GCF_003605405.2_ASM360540v2_genomic.fna/dqc_result.json
[2024-01-24 13:14:42,086] [INFO] DFAST_QC completed!
[2024-01-24 13:14:42,086] [INFO] Total running time: 0h1m30s