[2024-01-24 11:26:07,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:07,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:07,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference
[2024-01-24 11:26:08,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:08,911] [INFO] Task started: Prodigal
[2024-01-24 11:26:08,911] [INFO] Running command: gunzip -c /var/lib/cwl/stga6533d69-44f8-41d2-bf86-3b7bd232ea31/GCF_004126535.1_ASM412653v1_genomic.fna.gz | prodigal -d GCF_004126535.1_ASM412653v1_genomic.fna/cds.fna -a GCF_004126535.1_ASM412653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:18,421] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:18,421] [INFO] Task started: HMMsearch
[2024-01-24 11:26:18,421] [INFO] Running command: hmmsearch --tblout GCF_004126535.1_ASM412653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/reference_markers.hmm GCF_004126535.1_ASM412653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:18,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:18,730] [INFO] Found 6/6 markers.
[2024-01-24 11:26:18,756] [INFO] Query marker FASTA was written to GCF_004126535.1_ASM412653v1_genomic.fna/markers.fasta
[2024-01-24 11:26:18,757] [INFO] Task started: Blastn
[2024-01-24 11:26:18,757] [INFO] Running command: blastn -query GCF_004126535.1_ASM412653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/reference_markers.fasta -out GCF_004126535.1_ASM412653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:19,800] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:19,803] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:19,803] [INFO] Target genome list was writen to GCF_004126535.1_ASM412653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:19,832] [INFO] Task started: fastANI
[2024-01-24 11:26:19,833] [INFO] Running command: fastANI --query /var/lib/cwl/stga6533d69-44f8-41d2-bf86-3b7bd232ea31/GCF_004126535.1_ASM412653v1_genomic.fna.gz --refList GCF_004126535.1_ASM412653v1_genomic.fna/target_genomes.txt --output GCF_004126535.1_ASM412653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:30,298] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:30,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:30,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:30,315] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:30,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:30,316] [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
Propioniciclava flava	strain=VG341	GCA_004126535.1	2072026	2072026	type	True	100.0	990	990	95	conclusive
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	81.3028	608	990	95	below_threshold
Propioniciclava sinopodophylli	strain=KCTC 33808	GCA_004324755.1	1837344	1837344	type	True	79.9256	409	990	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	78.9756	343	990	95	below_threshold
Aestuariimicrobium ganziense	strain=YIM S02566	GCA_015352975.1	2773677	2773677	type	True	78.5004	185	990	95	below_threshold
Propioniciclava tarda	strain=DSM 22130	GCA_900182665.1	433330	433330	type	True	77.9639	221	990	95	below_threshold
Propionicimonas paludicola	strain=DSM 15597	GCA_002563675.1	185243	185243	type	True	77.7445	175	990	95	below_threshold
Naumannella cuiyingiana	strain=DSM 103164	GCA_013408305.1	1347891	1347891	type	True	77.2912	143	990	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.2136	119	990	95	below_threshold
Cutibacterium avidum	strain=ATCC 25577	GCA_000227295.1	33010	33010	type	True	77.0611	110	990	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	76.8929	194	990	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	76.4776	123	990	95	below_threshold
Actinopolymorpha rutila	strain=DSM 18448	GCA_013407855.1	446787	446787	type	True	76.2007	118	990	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	76.1721	129	990	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	76.0926	130	990	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	76.0108	128	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:30,319] [INFO] DFAST Taxonomy check result was written to GCF_004126535.1_ASM412653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:30,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:30,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:30,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/checkm_data
[2024-01-24 11:26:30,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:30,358] [INFO] Task started: CheckM
[2024-01-24 11:26:30,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004126535.1_ASM412653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004126535.1_ASM412653v1_genomic.fna/checkm_input GCF_004126535.1_ASM412653v1_genomic.fna/checkm_result
[2024-01-24 11:27:04,542] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:04,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:04,563] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:04,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:04,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004126535.1_ASM412653v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:04,565] [INFO] Task started: Blastn
[2024-01-24 11:27:04,565] [INFO] Running command: blastn -query GCF_004126535.1_ASM412653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86fc86ef-160d-4420-aa50-e8431ec7a68c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004126535.1_ASM412653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:06,100] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:06,105] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:06,106] [INFO] Target genome list was writen to GCF_004126535.1_ASM412653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:06,117] [INFO] Task started: fastANI
[2024-01-24 11:27:06,118] [INFO] Running command: fastANI --query /var/lib/cwl/stga6533d69-44f8-41d2-bf86-3b7bd232ea31/GCF_004126535.1_ASM412653v1_genomic.fna.gz --refList GCF_004126535.1_ASM412653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004126535.1_ASM412653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:15,465] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:15,481] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:15,482] [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_004126535.1	s__Brevilactibacter flavus	100.0	990	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011393335.1	s__Brevilactibacter coleopterorum	81.2916	609	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004324755.1	s__Brevilactibacter sinopodophylli	79.8859	412	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711325.1	s__Brevilactibacter sp016711325	79.5232	322	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017569205.1	s__Brevilactibacter sp014164685	79.5209	403	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	99.00	98.00	0.92	0.83	3	-
GCA_014858005.1	s__Brevilactibacter sp014858005	78.9756	343	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838755.1	s__Brevilactibacter sp012838755	78.9253	342	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826085.1	s__Nigerium massiliense	78.106	268	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Nigerium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012517965.1	s__Propioniciclava sp012517965	77.8563	260	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Propioniciclava	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408305.1	s__Naumannella cuiyingiana	77.2333	146	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Naumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	76.1753	127	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	76.1715	129	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_004348675.1	s__Micromonospora sp004348675	75.6877	114	990	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:15,484] [INFO] GTDB search result was written to GCF_004126535.1_ASM412653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:15,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:15,488] [INFO] DFAST_QC result json was written to GCF_004126535.1_ASM412653v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:15,488] [INFO] DFAST_QC completed!
[2024-01-24 11:27:15,488] [INFO] Total running time: 0h1m8s