[2024-01-24 14:37:46,909] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference
[2024-01-24 14:37:50,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,273] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,273] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf0d8dae-23e7-49c2-bcef-286c76cb9ea5/GCF_013761245.1_ASM1376124v1_genomic.fna.gz | prodigal -d GCF_013761245.1_ASM1376124v1_genomic.fna/cds.fna -a GCF_013761245.1_ASM1376124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:37:59,238] [INFO] Task succeeded: Prodigal
[2024-01-24 14:37:59,239] [INFO] Task started: HMMsearch
[2024-01-24 14:37:59,239] [INFO] Running command: hmmsearch --tblout GCF_013761245.1_ASM1376124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/reference_markers.hmm GCF_013761245.1_ASM1376124v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:37:59,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:37:59,513] [INFO] Found 6/6 markers.
[2024-01-24 14:37:59,569] [INFO] Query marker FASTA was written to GCF_013761245.1_ASM1376124v1_genomic.fna/markers.fasta
[2024-01-24 14:37:59,570] [INFO] Task started: Blastn
[2024-01-24 14:37:59,570] [INFO] Running command: blastn -query GCF_013761245.1_ASM1376124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/reference_markers.fasta -out GCF_013761245.1_ASM1376124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:00,266] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:00,269] [INFO] Selected 21 target genomes.
[2024-01-24 14:38:00,270] [INFO] Target genome list was writen to GCF_013761245.1_ASM1376124v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:00,279] [INFO] Task started: fastANI
[2024-01-24 14:38:00,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0d8dae-23e7-49c2-bcef-286c76cb9ea5/GCF_013761245.1_ASM1376124v1_genomic.fna.gz --refList GCF_013761245.1_ASM1376124v1_genomic.fna/target_genomes.txt --output GCF_013761245.1_ASM1376124v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:13,464] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:13,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:13,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:13,480] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:13,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:13,480] [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
Anoxybacillus caldiproteolyticus	strain=DSM 15730	GCA_013761245.1	247480	247480	type	True	100.0	1195	1196	95	conclusive
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	80.7797	538	1196	95	below_threshold
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	79.7603	472	1196	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	79.7443	504	1196	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	79.7335	513	1196	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	79.729	511	1196	95	below_threshold
Anoxybacillus tepidamans	strain=DSM 16325	GCA_014201465.1	265948	265948	type	True	79.572	471	1196	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	79.4949	510	1196	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=DSM 12041	GCA_014196025.1	81408	81408	type	True	79.4885	503	1196	95	below_threshold
Parageobacillus thermantarcticus	strain=M1	GCA_900111865.1	186116	186116	type	True	79.0877	480	1196	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	78.5996	384	1196	95	below_threshold
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	78.5985	382	1196	95	below_threshold
Anoxybacillus voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	78.5917	385	1196	95	below_threshold
Anoxybacillus ayderensis	strain=AB04	GCA_000833605.1	265546	265546	type	True	77.9913	234	1196	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	77.6454	216	1196	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.8588	59	1196	95	below_threshold
Bacillus massilionigeriensis	strain=Marseille-P2384	GCA_900117315.1	1805475	1805475	type	True	76.4426	61	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:13,482] [INFO] DFAST Taxonomy check result was written to GCF_013761245.1_ASM1376124v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:13,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:13,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:13,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/checkm_data
[2024-01-24 14:38:13,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:13,527] [INFO] Task started: CheckM
[2024-01-24 14:38:13,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013761245.1_ASM1376124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013761245.1_ASM1376124v1_genomic.fna/checkm_input GCF_013761245.1_ASM1376124v1_genomic.fna/checkm_result
[2024-01-24 14:38:45,562] [INFO] Task succeeded: CheckM
[2024-01-24 14:38:45,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:38:45,597] [INFO] ===== Completeness check finished =====
[2024-01-24 14:38:45,597] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:38:45,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013761245.1_ASM1376124v1_genomic.fna/markers.fasta)
[2024-01-24 14:38:45,599] [INFO] Task started: Blastn
[2024-01-24 14:38:45,599] [INFO] Running command: blastn -query GCF_013761245.1_ASM1376124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c60553c-99b4-4611-a0b4-7b0b4c356d90/dqc_reference/reference_markers_gtdb.fasta -out GCF_013761245.1_ASM1376124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:46,429] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:46,434] [INFO] Selected 22 target genomes.
[2024-01-24 14:38:46,434] [INFO] Target genome list was writen to GCF_013761245.1_ASM1376124v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:38:46,452] [INFO] Task started: fastANI
[2024-01-24 14:38:46,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf0d8dae-23e7-49c2-bcef-286c76cb9ea5/GCF_013761245.1_ASM1376124v1_genomic.fna.gz --refList GCF_013761245.1_ASM1376124v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013761245.1_ASM1376124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:03,758] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:03,785] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:03,786] [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_013761245.1	s__Anoxybacillus_C caldiproteolyticus	100.0	1195	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_C	95.0	99.29	99.25	0.94	0.93	3	conclusive
GCF_013760845.1	s__Anoxybacillus_B calidus	80.7993	538	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	80.0507	557	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259935.1	s__Anoxybacillus_B vitaminiphilus	79.7603	472	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688615.2	s__Parageobacillus toebii	79.7335	513	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_014201465.1	s__Anoxybacillus_A tepidamans	79.572	471	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	79.5654	532	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_000632515.1	s__Saccharococcus sp000632515	79.5371	492	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	79.4849	511	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
GCF_900111865.1	s__Parageobacillus thermantarcticus	79.0877	480	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196205.1	s__Anoxybacillus_A voinovskiensis	78.5952	385	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001634285.1	s__Anoxybacillus_A amylolyticus	78.5883	383	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196195.1	s__Anoxybacillus_A rupiensis	78.4754	406	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	98.88	98.54	0.93	0.92	7	-
GCF_014201585.1	s__Anoxybacillus tengchongensis	77.5103	225	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_014679505.1	s__Geobacillus sp002077765	76.9444	197	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	98.81	97.63	0.94	0.88	3	-
GCF_014773385.1	s__IB182487 sp014773385	76.7155	70	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__IB182487	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217655.1	s__Geobacillus thermocatenulatus	76.5833	168	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.1122	99.55	99.04	0.96	0.93	6	-
GCF_900117315.1	s__Bacillus_BE massilionigeriensis	76.4426	61	1196	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BE	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:03,788] [INFO] GTDB search result was written to GCF_013761245.1_ASM1376124v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:03,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:03,793] [INFO] DFAST_QC result json was written to GCF_013761245.1_ASM1376124v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:03,794] [INFO] DFAST_QC completed!
[2024-01-24 14:39:03,794] [INFO] Total running time: 0h1m17s