[2024-01-24 15:10:22,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference
[2024-01-24 15:10:24,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,488] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,488] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9d3af67-558a-4eed-a560-361b5fe6bbf6/GCF_005889735.1_ASM588973v1_genomic.fna.gz | prodigal -d GCF_005889735.1_ASM588973v1_genomic.fna/cds.fna -a GCF_005889735.1_ASM588973v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:56,842] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:56,843] [INFO] Task started: HMMsearch
[2024-01-24 15:10:56,843] [INFO] Running command: hmmsearch --tblout GCF_005889735.1_ASM588973v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/reference_markers.hmm GCF_005889735.1_ASM588973v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:57,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:57,315] [INFO] Found 6/6 markers.
[2024-01-24 15:10:57,406] [INFO] Query marker FASTA was written to GCF_005889735.1_ASM588973v1_genomic.fna/markers.fasta
[2024-01-24 15:10:57,406] [INFO] Task started: Blastn
[2024-01-24 15:10:57,407] [INFO] Running command: blastn -query GCF_005889735.1_ASM588973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/reference_markers.fasta -out GCF_005889735.1_ASM588973v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:58,769] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:58,773] [INFO] Selected 18 target genomes.
[2024-01-24 15:10:58,774] [INFO] Target genome list was writen to GCF_005889735.1_ASM588973v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:58,781] [INFO] Task started: fastANI
[2024-01-24 15:10:58,781] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d3af67-558a-4eed-a560-361b5fe6bbf6/GCF_005889735.1_ASM588973v1_genomic.fna.gz --refList GCF_005889735.1_ASM588973v1_genomic.fna/target_genomes.txt --output GCF_005889735.1_ASM588973v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:48,942] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:48,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:48,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:48,957] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:48,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:48,957] [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
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	100.0	3467	3488	95	conclusive
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	90.8424	2502	3488	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	88.6038	2407	3488	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	86.2556	2328	3488	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	86.1003	2295	3488	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.9743	1939	3488	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	85.9606	2231	3488	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.6454	2318	3488	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.5106	1996	3488	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.4459	2085	3488	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.3795	2100	3488	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.3074	1987	3488	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	85.288	1914	3488	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	85.2609	1945	3488	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	84.904	1879	3488	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.8385	1183	3488	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.3823	1976	3488	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	82.7203	1786	3488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:48,959] [INFO] DFAST Taxonomy check result was written to GCF_005889735.1_ASM588973v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:48,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:48,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:48,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/checkm_data
[2024-01-24 15:11:48,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:49,060] [INFO] Task started: CheckM
[2024-01-24 15:11:49,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005889735.1_ASM588973v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005889735.1_ASM588973v1_genomic.fna/checkm_input GCF_005889735.1_ASM588973v1_genomic.fna/checkm_result
[2024-01-24 15:13:23,399] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:23,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:23,426] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:23,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:23,427] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005889735.1_ASM588973v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:23,427] [INFO] Task started: Blastn
[2024-01-24 15:13:23,427] [INFO] Running command: blastn -query GCF_005889735.1_ASM588973v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb613fa8c-337b-46e7-86f9-8ad514ab9d94/dqc_reference/reference_markers_gtdb.fasta -out GCF_005889735.1_ASM588973v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:25,414] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:25,418] [INFO] Selected 13 target genomes.
[2024-01-24 15:13:25,418] [INFO] Target genome list was writen to GCF_005889735.1_ASM588973v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:25,426] [INFO] Task started: fastANI
[2024-01-24 15:13:25,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9d3af67-558a-4eed-a560-361b5fe6bbf6/GCF_005889735.1_ASM588973v1_genomic.fna.gz --refList GCF_005889735.1_ASM588973v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005889735.1_ASM588973v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:14:03,308] [INFO] Task succeeded: fastANI
[2024-01-24 15:14:03,319] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:14:03,320] [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_005889735.1	s__Nonomuraea turkmeniaca	100.0	3467	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004011505.1	s__Nonomuraea polychroma	90.8412	2501	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	88.5983	2407	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	88.1993	2408	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	86.2644	2325	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	86.1258	2290	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889725.1	s__Nonomuraea zeae	85.9931	2226	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645445.1	s__Nonomuraea cypriaca	85.9492	1943	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	85.5816	2317	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	85.5141	1994	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_000379885.1	s__Nonomuraea coxensis	85.2936	1912	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348995.1	s__Nonomuraea terrae	84.908	1878	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	82.7571	1775	3488	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:14:03,321] [INFO] GTDB search result was written to GCF_005889735.1_ASM588973v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:14:03,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:14:03,326] [INFO] DFAST_QC result json was written to GCF_005889735.1_ASM588973v1_genomic.fna/dqc_result.json
[2024-01-24 15:14:03,326] [INFO] DFAST_QC completed!
[2024-01-24 15:14:03,326] [INFO] Total running time: 0h3m40s