[2024-01-25 17:43:50,703] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference
[2024-01-25 17:43:51,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,795] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,795] [INFO] Running command: gunzip -c /var/lib/cwl/stge511fcf6-7042-429a-9623-50358578b8c4/GCF_014201465.1_ASM1420146v1_genomic.fna.gz | prodigal -d GCF_014201465.1_ASM1420146v1_genomic.fna/cds.fna -a GCF_014201465.1_ASM1420146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:59,124] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:59,124] [INFO] Task started: HMMsearch
[2024-01-25 17:43:59,124] [INFO] Running command: hmmsearch --tblout GCF_014201465.1_ASM1420146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/reference_markers.hmm GCF_014201465.1_ASM1420146v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:59,340] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:59,341] [INFO] Found 6/6 markers.
[2024-01-25 17:43:59,373] [INFO] Query marker FASTA was written to GCF_014201465.1_ASM1420146v1_genomic.fna/markers.fasta
[2024-01-25 17:43:59,373] [INFO] Task started: Blastn
[2024-01-25 17:43:59,373] [INFO] Running command: blastn -query GCF_014201465.1_ASM1420146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/reference_markers.fasta -out GCF_014201465.1_ASM1420146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:59,923] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:59,927] [INFO] Selected 14 target genomes.
[2024-01-25 17:43:59,927] [INFO] Target genome list was writen to GCF_014201465.1_ASM1420146v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:59,945] [INFO] Task started: fastANI
[2024-01-25 17:43:59,945] [INFO] Running command: fastANI --query /var/lib/cwl/stge511fcf6-7042-429a-9623-50358578b8c4/GCF_014201465.1_ASM1420146v1_genomic.fna.gz --refList GCF_014201465.1_ASM1420146v1_genomic.fna/target_genomes.txt --output GCF_014201465.1_ASM1420146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:10,861] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:10,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:10,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:10,869] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:10,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:10,869] [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 tepidamans	strain=DSM 16325	GCA_014201465.1	265948	265948	type	True	100.0	1099	1104	95	conclusive
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	83.1868	666	1104	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	82.7249	664	1104	95	below_threshold
Anoxybacillus voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	82.5918	676	1104	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	79.7365	310	1104	95	below_threshold
Anoxybacillus caldiproteolyticus	strain=DSM 15730	GCA_013761245.1	247480	247480	type	True	79.5887	478	1104	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	79.292	314	1104	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	79.2427	305	1104	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.803	53	1104	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.1899	51	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:10,870] [INFO] DFAST Taxonomy check result was written to GCF_014201465.1_ASM1420146v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:10,871] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:10,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:10,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/checkm_data
[2024-01-25 17:44:10,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:10,908] [INFO] Task started: CheckM
[2024-01-25 17:44:10,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201465.1_ASM1420146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201465.1_ASM1420146v1_genomic.fna/checkm_input GCF_014201465.1_ASM1420146v1_genomic.fna/checkm_result
[2024-01-25 17:44:37,297] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:37,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:37,323] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:37,323] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:37,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201465.1_ASM1420146v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:37,323] [INFO] Task started: Blastn
[2024-01-25 17:44:37,323] [INFO] Running command: blastn -query GCF_014201465.1_ASM1420146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c5dc3ca-0688-4366-9d09-3240a292cc94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201465.1_ASM1420146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:38,142] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:38,145] [INFO] Selected 12 target genomes.
[2024-01-25 17:44:38,145] [INFO] Target genome list was writen to GCF_014201465.1_ASM1420146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:38,160] [INFO] Task started: fastANI
[2024-01-25 17:44:38,160] [INFO] Running command: fastANI --query /var/lib/cwl/stge511fcf6-7042-429a-9623-50358578b8c4/GCF_014201465.1_ASM1420146v1_genomic.fna.gz --refList GCF_014201465.1_ASM1420146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201465.1_ASM1420146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:48,665] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:48,672] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:48,672] [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_014201465.1	s__Anoxybacillus_A tepidamans	100.0	1099	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001634285.1	s__Anoxybacillus_A amylolyticus	83.2463	663	1104	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_014196205.1	s__Anoxybacillus_A voinovskiensis	82.747	663	1104	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_000620165.1	s__Anoxybacillus_A tepidamans_A	80.4503	577	1104	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_000836725.1	s__Anoxybacillus thermarum	79.708	311	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013761245.1	s__Anoxybacillus_C caldiproteolyticus	79.5671	480	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_C	95.0	99.29	99.25	0.94	0.93	3	-
GCA_002243705.1	s__Anoxybacillus flavithermus	79.5043	319	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_002197485.1	s__Anoxybacillus flavithermus_G	79.4427	316	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	79.3608	293	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCF_001187595.1	s__Anoxybacillus gonensis	79.3049	314	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_014196195.1	s__Anoxybacillus_A rupiensis	79.2271	508	1104	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_007995155.1	s__Cytobacillus dafuensis	76.803	53	1104	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:48,675] [INFO] GTDB search result was written to GCF_014201465.1_ASM1420146v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:48,676] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:48,678] [INFO] DFAST_QC result json was written to GCF_014201465.1_ASM1420146v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:48,679] [INFO] DFAST_QC completed!
[2024-01-25 17:44:48,679] [INFO] Total running time: 0h0m58s