[2024-01-24 13:45:58,861] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:58,863] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:58,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference
[2024-01-24 13:46:00,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:00,170] [INFO] Task started: Prodigal
[2024-01-24 13:46:00,171] [INFO] Running command: gunzip -c /var/lib/cwl/stge0086588-b8cb-4ec4-a077-f0eccb450a3a/GCF_022048975.1_ASM2204897v1_genomic.fna.gz | prodigal -d GCF_022048975.1_ASM2204897v1_genomic.fna/cds.fna -a GCF_022048975.1_ASM2204897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:10,857] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:10,858] [INFO] Task started: HMMsearch
[2024-01-24 13:46:10,858] [INFO] Running command: hmmsearch --tblout GCF_022048975.1_ASM2204897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/reference_markers.hmm GCF_022048975.1_ASM2204897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:11,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:11,206] [INFO] Found 6/6 markers.
[2024-01-24 13:46:11,267] [INFO] Query marker FASTA was written to GCF_022048975.1_ASM2204897v1_genomic.fna/markers.fasta
[2024-01-24 13:46:11,268] [INFO] Task started: Blastn
[2024-01-24 13:46:11,268] [INFO] Running command: blastn -query GCF_022048975.1_ASM2204897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/reference_markers.fasta -out GCF_022048975.1_ASM2204897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:11,906] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:11,909] [INFO] Selected 23 target genomes.
[2024-01-24 13:46:11,910] [INFO] Target genome list was writen to GCF_022048975.1_ASM2204897v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:11,949] [INFO] Task started: fastANI
[2024-01-24 13:46:11,950] [INFO] Running command: fastANI --query /var/lib/cwl/stge0086588-b8cb-4ec4-a077-f0eccb450a3a/GCF_022048975.1_ASM2204897v1_genomic.fna.gz --refList GCF_022048975.1_ASM2204897v1_genomic.fna/target_genomes.txt --output GCF_022048975.1_ASM2204897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:26,098] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:26,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:26,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:26,102] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:26,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:26,103] [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
Sporosarcina luteola	strain=NBRC 105378	GCA_007991495.1	582850	582850	type	True	78.0303	280	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:26,104] [INFO] DFAST Taxonomy check result was written to GCF_022048975.1_ASM2204897v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:26,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:26,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:26,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/checkm_data
[2024-01-24 13:46:26,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:26,160] [INFO] Task started: CheckM
[2024-01-24 13:46:26,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022048975.1_ASM2204897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022048975.1_ASM2204897v1_genomic.fna/checkm_input GCF_022048975.1_ASM2204897v1_genomic.fna/checkm_result
[2024-01-24 13:47:03,906] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:03,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:03,925] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:03,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:03,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022048975.1_ASM2204897v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:03,926] [INFO] Task started: Blastn
[2024-01-24 13:47:03,926] [INFO] Running command: blastn -query GCF_022048975.1_ASM2204897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2f010a5-d78d-49b3-9516-17c3ce79604b/dqc_reference/reference_markers_gtdb.fasta -out GCF_022048975.1_ASM2204897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:04,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:04,783] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:04,783] [INFO] Target genome list was writen to GCF_022048975.1_ASM2204897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:04,824] [INFO] Task started: fastANI
[2024-01-24 13:47:04,825] [INFO] Running command: fastANI --query /var/lib/cwl/stge0086588-b8cb-4ec4-a077-f0eccb450a3a/GCF_022048975.1_ASM2204897v1_genomic.fna.gz --refList GCF_022048975.1_ASM2204897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022048975.1_ASM2204897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:20,334] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:20,345] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:20,345] [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_017498505.1	s__Sporosarcina sp017498505	84.3125	983	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204635.1	s__Sporosarcina luteola_A	83.442	915	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001531445.1	s__Sporosarcina koreensis_C	78.1447	284	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991495.1	s__Sporosarcina luteola	78.0344	281	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077155.1	s__Sporosarcina sp002077155	77.9022	97	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.91	98.90	0.90	0.90	3	-
GCF_000826145.2	s__Sporosarcina koreensis_B	77.6866	109	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590685.1	s__Sporosarcina psychrophila	77.5493	135	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	98.26	98.26	0.89	0.89	2	-
GCF_016820585.1	s__Sporosarcina sp016820585	77.4705	137	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009651005.1	s__Sporosarcina sp009651005	77.3732	109	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017347095.1	s__Sporosarcina sp017347095	77.1961	127	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282005.1	s__Sporosarcina sp014282005	76.8707	126	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	96.23	96.23	0.81	0.81	2	-
GCF_009650995.1	s__Sporosarcina sp009650995	76.8337	124	1307	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Sporosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:20,348] [INFO] GTDB search result was written to GCF_022048975.1_ASM2204897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:20,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:20,353] [INFO] DFAST_QC result json was written to GCF_022048975.1_ASM2204897v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:20,353] [INFO] DFAST_QC completed!
[2024-01-24 13:47:20,353] [INFO] Total running time: 0h1m21s