[2024-01-24 11:34:43,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,084] [INFO] DQC Reference Directory: /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference
[2024-01-24 11:34:44,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,425] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg991dde6d-9806-4924-9d71-e9a11a101f44/GCF_001940455.1_ASM194045v1_genomic.fna.gz | prodigal -d GCF_001940455.1_ASM194045v1_genomic.fna/cds.fna -a GCF_001940455.1_ASM194045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:09,862] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:09,863] [INFO] Task started: HMMsearch
[2024-01-24 11:35:09,863] [INFO] Running command: hmmsearch --tblout GCF_001940455.1_ASM194045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/reference_markers.hmm GCF_001940455.1_ASM194045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:10,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:10,266] [INFO] Found 6/6 markers.
[2024-01-24 11:35:10,337] [INFO] Query marker FASTA was written to GCF_001940455.1_ASM194045v1_genomic.fna/markers.fasta
[2024-01-24 11:35:10,337] [INFO] Task started: Blastn
[2024-01-24 11:35:10,337] [INFO] Running command: blastn -query GCF_001940455.1_ASM194045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/reference_markers.fasta -out GCF_001940455.1_ASM194045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:11,764] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:11,767] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:11,767] [INFO] Target genome list was writen to GCF_001940455.1_ASM194045v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:11,774] [INFO] Task started: fastANI
[2024-01-24 11:35:11,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg991dde6d-9806-4924-9d71-e9a11a101f44/GCF_001940455.1_ASM194045v1_genomic.fna.gz --refList GCF_001940455.1_ASM194045v1_genomic.fna/target_genomes.txt --output GCF_001940455.1_ASM194045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,378] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,395] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:46,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:46,395] [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
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	99.998	2454	2466	95	conclusive
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	84.2239	1495	2466	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	83.6822	1395	2466	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	81.3792	1185	2466	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.362	1212	2466	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	81.3288	1195	2466	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	81.0796	1288	2466	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	81.0291	1202	2466	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	80.9563	1221	2466	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	80.9341	1215	2466	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	78.9332	1122	2466	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	78.7854	1029	2466	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	78.6862	1027	2466	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.4766	990	2466	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.1882	901	2466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,398] [INFO] DFAST Taxonomy check result was written to GCF_001940455.1_ASM194045v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/checkm_data
[2024-01-24 11:35:46,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,469] [INFO] Task started: CheckM
[2024-01-24 11:35:46,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001940455.1_ASM194045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001940455.1_ASM194045v1_genomic.fna/checkm_input GCF_001940455.1_ASM194045v1_genomic.fna/checkm_result
[2024-01-24 11:37:34,168] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:34,169] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:34,192] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:34,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:34,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001940455.1_ASM194045v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:34,193] [INFO] Task started: Blastn
[2024-01-24 11:37:34,193] [INFO] Running command: blastn -query GCF_001940455.1_ASM194045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf30bb061-860b-47dd-92b9-cc38e40e1e23/dqc_reference/reference_markers_gtdb.fasta -out GCF_001940455.1_ASM194045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:36,241] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:36,245] [INFO] Selected 13 target genomes.
[2024-01-24 11:37:36,246] [INFO] Target genome list was writen to GCF_001940455.1_ASM194045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:36,256] [INFO] Task started: fastANI
[2024-01-24 11:37:36,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg991dde6d-9806-4924-9d71-e9a11a101f44/GCF_001940455.1_ASM194045v1_genomic.fna.gz --refList GCF_001940455.1_ASM194045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001940455.1_ASM194045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:05,283] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:05,296] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:05,296] [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_001940455.1	s__Actinokineospora bangkokensis	99.998	2454	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003182415.1	s__Actinokineospora mzabensis	84.2308	1561	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_009745975.1	s__Actinokineospora pegani	83.6832	1398	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	81.3609	1187	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	81.2972	1203	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	81.2585	1215	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_000374445.1	s__Actinokineospora enzanensis	81.064	1195	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	81.0463	1295	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	80.9453	1225	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	78.944	1122	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	78.781	1030	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984155.1	s__Kibdelosporangium sp001984155	78.1088	984	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887735.1	s__Stenotrophomonas bentonitica_A	74.9495	183	2466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	97.97	97.41	0.91	0.87	8	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:05,298] [INFO] GTDB search result was written to GCF_001940455.1_ASM194045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:05,299] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:05,302] [INFO] DFAST_QC result json was written to GCF_001940455.1_ASM194045v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:05,302] [INFO] DFAST_QC completed!
[2024-01-24 11:38:05,302] [INFO] Total running time: 0h3m22s