[2024-01-24 13:33:41,331] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,333] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference
[2024-01-24 13:33:42,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,721] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg33e47bae-3c54-4726-afe4-204b779c267d/GCF_021172045.1_ASM2117204v1_genomic.fna.gz | prodigal -d GCF_021172045.1_ASM2117204v1_genomic.fna/cds.fna -a GCF_021172045.1_ASM2117204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:59,099] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:59,100] [INFO] Task started: HMMsearch
[2024-01-24 13:33:59,100] [INFO] Running command: hmmsearch --tblout GCF_021172045.1_ASM2117204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/reference_markers.hmm GCF_021172045.1_ASM2117204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:59,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:59,408] [INFO] Found 6/6 markers.
[2024-01-24 13:33:59,461] [INFO] Query marker FASTA was written to GCF_021172045.1_ASM2117204v1_genomic.fna/markers.fasta
[2024-01-24 13:33:59,461] [INFO] Task started: Blastn
[2024-01-24 13:33:59,461] [INFO] Running command: blastn -query GCF_021172045.1_ASM2117204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/reference_markers.fasta -out GCF_021172045.1_ASM2117204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:00,174] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:00,178] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:00,178] [INFO] Target genome list was writen to GCF_021172045.1_ASM2117204v1_genomic.fna/target_genomes.txt
[2024-01-24 13:34:00,187] [INFO] Task started: fastANI
[2024-01-24 13:34:00,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e47bae-3c54-4726-afe4-204b779c267d/GCF_021172045.1_ASM2117204v1_genomic.fna.gz --refList GCF_021172045.1_ASM2117204v1_genomic.fna/target_genomes.txt --output GCF_021172045.1_ASM2117204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:13,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:13,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:13,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:13,046] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:34:13,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:13,047] [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
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	100.0	1984	1984	95	conclusive
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	78.5649	808	1984	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	77.8948	794	1984	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	77.8546	729	1984	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	77.6003	834	1984	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	77.1626	773	1984	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	76.6011	632	1984	95	below_threshold
Amnibacterium kyonggiense	strain=DSM 24782	GCA_004364555.1	595671	595671	type	True	75.1112	360	1984	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	75.1032	360	1984	95	below_threshold
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	75.034	333	1984	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,048] [INFO] DFAST Taxonomy check result was written to GCF_021172045.1_ASM2117204v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:13,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:13,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:13,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/checkm_data
[2024-01-24 13:34:13,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:13,104] [INFO] Task started: CheckM
[2024-01-24 13:34:13,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021172045.1_ASM2117204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021172045.1_ASM2117204v1_genomic.fna/checkm_input GCF_021172045.1_ASM2117204v1_genomic.fna/checkm_result
[2024-01-24 13:35:40,257] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:40,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:40,280] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:40,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:40,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021172045.1_ASM2117204v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:40,281] [INFO] Task started: Blastn
[2024-01-24 13:35:40,281] [INFO] Running command: blastn -query GCF_021172045.1_ASM2117204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd17f83c6-87e6-4cc0-8bbd-a500ec22ce32/dqc_reference/reference_markers_gtdb.fasta -out GCF_021172045.1_ASM2117204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:41,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:41,406] [INFO] Selected 18 target genomes.
[2024-01-24 13:35:41,406] [INFO] Target genome list was writen to GCF_021172045.1_ASM2117204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:41,528] [INFO] Task started: fastANI
[2024-01-24 13:35:41,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg33e47bae-3c54-4726-afe4-204b779c267d/GCF_021172045.1_ASM2117204v1_genomic.fna.gz --refList GCF_021172045.1_ASM2117204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021172045.1_ASM2117204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:59,420] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:59,440] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:35:59,440] [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
GCA_013813955.1	s__CADCVQ01 sp013813955	78.9395	308	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888335.1	s__VAWY01 sp005888335	78.8873	791	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__VAWY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970665.1	s__Baekduia soli	78.5297	814	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	78.4033	626	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	78.4005	605	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	78.3405	738	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806205.1	s__SEOHO-28 sp902806205	78.0754	483	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882425.1	s__F1-60-MAGs163 sp017882425	78.055	466	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__F1-60-MAGs163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815355.1	s__Palsa-744 sp013815355	77.9478	328	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199525.1	s__Conexibacter arvalis	77.9221	786	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044185.1	s__SEOHO-28 sp003044185	77.8698	726	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCF_000424625.1	s__Baekduia woesei_A	77.8695	784	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882455.1	s__Palsa-744 sp017882455	77.854	370	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462625.1	s__SYBY01 sp016462625	77.7831	549	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SYBY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806215.1	s__CADCVT01 sp902806215	77.7084	518	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240115.1	s__Palsa-465 sp019240115	77.6018	526	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423665.1	s__Solirubrobacter soli	77.1822	872	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016929195.1	s__JACVRW01 sp016929195	76.9745	429	1984	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Thermoleophilaceae;g__JACVRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:59,442] [INFO] GTDB search result was written to GCF_021172045.1_ASM2117204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:59,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:59,447] [INFO] DFAST_QC result json was written to GCF_021172045.1_ASM2117204v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:59,448] [INFO] DFAST_QC completed!
[2024-01-24 13:35:59,448] [INFO] Total running time: 0h2m18s