[2024-01-24 13:13:23,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:23,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:23,629] [INFO] DQC Reference Directory: /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference
[2024-01-24 13:13:24,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:24,937] [INFO] Task started: Prodigal
[2024-01-24 13:13:24,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd02308b-bd2b-4d47-9525-1f2a20fac084/GCF_013410545.1_ASM1341054v1_genomic.fna.gz | prodigal -d GCF_013410545.1_ASM1341054v1_genomic.fna/cds.fna -a GCF_013410545.1_ASM1341054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:37,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:37,142] [INFO] Task started: HMMsearch
[2024-01-24 13:13:37,142] [INFO] Running command: hmmsearch --tblout GCF_013410545.1_ASM1341054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/reference_markers.hmm GCF_013410545.1_ASM1341054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:37,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:37,471] [INFO] Found 6/6 markers.
[2024-01-24 13:13:37,511] [INFO] Query marker FASTA was written to GCF_013410545.1_ASM1341054v1_genomic.fna/markers.fasta
[2024-01-24 13:13:37,511] [INFO] Task started: Blastn
[2024-01-24 13:13:37,512] [INFO] Running command: blastn -query GCF_013410545.1_ASM1341054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/reference_markers.fasta -out GCF_013410545.1_ASM1341054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:38,748] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:38,752] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:38,752] [INFO] Target genome list was writen to GCF_013410545.1_ASM1341054v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:38,786] [INFO] Task started: fastANI
[2024-01-24 13:13:38,786] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd02308b-bd2b-4d47-9525-1f2a20fac084/GCF_013410545.1_ASM1341054v1_genomic.fna.gz --refList GCF_013410545.1_ASM1341054v1_genomic.fna/target_genomes.txt --output GCF_013410545.1_ASM1341054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:53,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:53,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:53,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:53,519] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:53,519] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:53,519] [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
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_013410545.1	587635	587635	type	True	100.0	1327	1328	95	conclusive
Pseudoclavibacter chungangensis	strain=DSM 23821	GCA_008831135.1	587635	587635	type	True	99.9561	1268	1328	95	conclusive
Pseudoclavibacter helvolus	strain=DSM 20419	GCA_014191305.1	255205	255205	type	True	79.4475	437	1328	95	below_threshold
Pseudoclavibacter terrae	strain=THG-MD12	GCA_008831075.1	1530195	1530195	type	True	79.1575	435	1328	95	below_threshold
Pseudoclavibacter endophyticus	strain=CGMCC 1.15081	GCA_014640595.1	1778590	1778590	type	True	78.823	444	1328	95	below_threshold
Pseudoclavibacter endophyticus	strain=EGI 60007	GCA_008831085.1	1778590	1778590	type	True	78.7961	445	1328	95	below_threshold
Gulosibacter molinativorax	strain=ON4	GCA_003010915.2	256821	256821	type	True	78.24	281	1328	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	78.0967	302	1328	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	78.0151	389	1328	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	78.0122	430	1328	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	77.9375	418	1328	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	77.8959	433	1328	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	77.84	293	1328	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.8223	411	1328	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.7815	413	1328	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	77.778	344	1328	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.9902	337	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:53,521] [INFO] DFAST Taxonomy check result was written to GCF_013410545.1_ASM1341054v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:53,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:53,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:53,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/checkm_data
[2024-01-24 13:13:53,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:53,573] [INFO] Task started: CheckM
[2024-01-24 13:13:53,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013410545.1_ASM1341054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013410545.1_ASM1341054v1_genomic.fna/checkm_input GCF_013410545.1_ASM1341054v1_genomic.fna/checkm_result
[2024-01-24 13:15:09,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:09,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:09,789] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:09,789] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:09,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013410545.1_ASM1341054v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:09,790] [INFO] Task started: Blastn
[2024-01-24 13:15:09,790] [INFO] Running command: blastn -query GCF_013410545.1_ASM1341054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18c8214-5330-4ad9-bb5e-431f1b612246/dqc_reference/reference_markers_gtdb.fasta -out GCF_013410545.1_ASM1341054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:11,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:11,726] [INFO] Selected 14 target genomes.
[2024-01-24 13:15:11,726] [INFO] Target genome list was writen to GCF_013410545.1_ASM1341054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:11,751] [INFO] Task started: fastANI
[2024-01-24 13:15:11,752] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd02308b-bd2b-4d47-9525-1f2a20fac084/GCF_013410545.1_ASM1341054v1_genomic.fna.gz --refList GCF_013410545.1_ASM1341054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013410545.1_ASM1341054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:22,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:22,217] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:22,218] [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_013410545.1	s__Pseudoclavibacter chungangensis	100.0	1327	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_910822395.1	s__Pseudoclavibacter sp910822395	80.0423	449	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831075.1	s__Pseudoclavibacter terrae	79.1576	435	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	96.82	96.82	0.88	0.88	2	-
GCF_002931555.1	s__Pseudoclavibacter sp002931555	79.1461	447	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	98.27	98.05	0.90	0.88	3	-
GCF_002931055.1	s__Pseudoclavibacter sp002931055	79.1289	426	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	97.65	95.42	0.90	0.86	11	-
GCF_008831085.1	s__Pseudoclavibacter endophyticus	78.8338	441	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Pseudoclavibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012719255.1	s__Gulosibacter sp012719255	78.8028	345	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626105.1	s__Gulosibacter sp900626105	78.5255	363	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	98.80	98.80	0.92	0.92	2	-
GCF_900163695.1	s__Gulosibacter sp900163695	78.4654	409	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Gulosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	78.0609	424	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645235.1	s__Agrococcus terreus	78.0329	387	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	77.8881	424	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113185.1	s__Agromyces sp900113185	77.8263	424	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212695.1	s__Cellulomonas fimi	76.534	382	1328	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:22,220] [INFO] GTDB search result was written to GCF_013410545.1_ASM1341054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:22,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:22,224] [INFO] DFAST_QC result json was written to GCF_013410545.1_ASM1341054v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:22,224] [INFO] DFAST_QC completed!
[2024-01-24 13:15:22,224] [INFO] Total running time: 0h1m59s