[2024-01-24 14:47:19,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,698] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference
[2024-01-24 14:47:21,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,061] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,061] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9508914-ed53-4a88-a3d3-8c753b39779c/GCF_014873145.1_ASM1487314v1_genomic.fna.gz | prodigal -d GCF_014873145.1_ASM1487314v1_genomic.fna/cds.fna -a GCF_014873145.1_ASM1487314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:11,149] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:11,150] [INFO] Task started: HMMsearch
[2024-01-24 14:48:11,150] [INFO] Running command: hmmsearch --tblout GCF_014873145.1_ASM1487314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/reference_markers.hmm GCF_014873145.1_ASM1487314v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:11,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:11,658] [INFO] Found 6/6 markers.
[2024-01-24 14:48:11,757] [INFO] Query marker FASTA was written to GCF_014873145.1_ASM1487314v1_genomic.fna/markers.fasta
[2024-01-24 14:48:11,757] [INFO] Task started: Blastn
[2024-01-24 14:48:11,757] [INFO] Running command: blastn -query GCF_014873145.1_ASM1487314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/reference_markers.fasta -out GCF_014873145.1_ASM1487314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:13,135] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:13,140] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:13,141] [INFO] Target genome list was writen to GCF_014873145.1_ASM1487314v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:13,146] [INFO] Task started: fastANI
[2024-01-24 14:48:13,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9508914-ed53-4a88-a3d3-8c753b39779c/GCF_014873145.1_ASM1487314v1_genomic.fna.gz --refList GCF_014873145.1_ASM1487314v1_genomic.fna/target_genomes.txt --output GCF_014873145.1_ASM1487314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:49:06,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:06,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:49:06,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:49:06,330] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:49:06,330] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:49:06,330] [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 angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	100.0	4363	4364	95	conclusive
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	94.8784	3556	4364	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	87.7403	2528	4364	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	87.7114	2557	4364	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	86.3556	2573	4364	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	86.2986	2620	4364	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	86.1174	2278	4364	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.9735	2793	4364	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.9125	2327	4364	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.8952	2552	4364	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.7786	2735	4364	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.71	2277	4364	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.4177	2587	4364	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.4219	2395	4364	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.1211	1318	4364	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.3868	2186	4364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:49:06,332] [INFO] DFAST Taxonomy check result was written to GCF_014873145.1_ASM1487314v1_genomic.fna/tc_result.tsv
[2024-01-24 14:49:06,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:49:06,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:49:06,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/checkm_data
[2024-01-24 14:49:06,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:49:06,461] [INFO] Task started: CheckM
[2024-01-24 14:49:06,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014873145.1_ASM1487314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014873145.1_ASM1487314v1_genomic.fna/checkm_input GCF_014873145.1_ASM1487314v1_genomic.fna/checkm_result
[2024-01-24 14:52:05,498] [INFO] Task succeeded: CheckM
[2024-01-24 14:52:05,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.30%
Strain heterogeneity: 44.44%
--------------------------------------------------------------------------------
[2024-01-24 14:52:05,532] [INFO] ===== Completeness check finished =====
[2024-01-24 14:52:05,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:52:05,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014873145.1_ASM1487314v1_genomic.fna/markers.fasta)
[2024-01-24 14:52:05,534] [INFO] Task started: Blastn
[2024-01-24 14:52:05,534] [INFO] Running command: blastn -query GCF_014873145.1_ASM1487314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d150491-cffe-4f50-b47a-433ef6bd46b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014873145.1_ASM1487314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:52:07,719] [INFO] Task succeeded: Blastn
[2024-01-24 14:52:07,724] [INFO] Selected 14 target genomes.
[2024-01-24 14:52:07,725] [INFO] Target genome list was writen to GCF_014873145.1_ASM1487314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:52:07,733] [INFO] Task started: fastANI
[2024-01-24 14:52:07,734] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9508914-ed53-4a88-a3d3-8c753b39779c/GCF_014873145.1_ASM1487314v1_genomic.fna.gz --refList GCF_014873145.1_ASM1487314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014873145.1_ASM1487314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:52:57,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:52:57,584] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:52:57,585] [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_014873145.1	s__Nonomuraea angiospora	100.0	4364	4364	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_014204795.1	s__Nonomuraea jabiensis	94.8949	3554	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	87.7026	2534	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_005893125.1	s__Nonomuraea sp005893125	86.3601	2573	4364	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	86.2866	2623	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	86.0841	2286	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	86.0022	2784	4364	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	85.9426	2322	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.8929	2571	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	85.8815	2551	4364	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	85.7768	2735	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	85.4027	2591	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	85.3195	2642	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.4315	2390	4364	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:52:57,586] [INFO] GTDB search result was written to GCF_014873145.1_ASM1487314v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:52:57,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:52:57,591] [INFO] DFAST_QC result json was written to GCF_014873145.1_ASM1487314v1_genomic.fna/dqc_result.json
[2024-01-24 14:52:57,591] [INFO] DFAST_QC completed!
[2024-01-24 14:52:57,591] [INFO] Total running time: 0h5m38s