[2024-01-24 15:19:04,429] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,431] [INFO] DQC Reference Directory: /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference
[2024-01-24 15:19:05,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,682] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg889c689f-0d52-4cce-abbe-cfee0f2c1f53/GCF_005893125.1_ASM589312v1_genomic.fna.gz | prodigal -d GCF_005893125.1_ASM589312v1_genomic.fna/cds.fna -a GCF_005893125.1_ASM589312v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:44,516] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:44,517] [INFO] Task started: HMMsearch
[2024-01-24 15:19:44,517] [INFO] Running command: hmmsearch --tblout GCF_005893125.1_ASM589312v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/reference_markers.hmm GCF_005893125.1_ASM589312v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:45,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:45,008] [INFO] Found 6/6 markers.
[2024-01-24 15:19:45,112] [INFO] Query marker FASTA was written to GCF_005893125.1_ASM589312v1_genomic.fna/markers.fasta
[2024-01-24 15:19:45,112] [INFO] Task started: Blastn
[2024-01-24 15:19:45,112] [INFO] Running command: blastn -query GCF_005893125.1_ASM589312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/reference_markers.fasta -out GCF_005893125.1_ASM589312v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:46,376] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:46,379] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:46,380] [INFO] Target genome list was writen to GCF_005893125.1_ASM589312v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:46,393] [INFO] Task started: fastANI
[2024-01-24 15:19:46,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg889c689f-0d52-4cce-abbe-cfee0f2c1f53/GCF_005893125.1_ASM589312v1_genomic.fna.gz --refList GCF_005893125.1_ASM589312v1_genomic.fna/target_genomes.txt --output GCF_005893125.1_ASM589312v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:36,671] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:36,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:36,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:36,690] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:36,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:36,690] [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 basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	100.0	4441	4469	95	conclusive
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	88.4585	2424	4469	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	88.1878	2644	4469	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	86.343	2611	4469	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	86.2722	2561	4469	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	86.1222	2461	4469	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	86.0272	2618	4469	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.6594	2158	4469	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.5784	2506	4469	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.532	2154	4469	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.4081	2300	4469	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.3467	2277	4469	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	85.175	2042	4469	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	85.0942	2023	4469	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	85.0506	2059	4469	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.96	1231	4469	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.5605	2251	4469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:36,695] [INFO] DFAST Taxonomy check result was written to GCF_005893125.1_ASM589312v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:36,696] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:36,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:36,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/checkm_data
[2024-01-24 15:20:36,701] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:36,827] [INFO] Task started: CheckM
[2024-01-24 15:20:36,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005893125.1_ASM589312v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005893125.1_ASM589312v1_genomic.fna/checkm_input GCF_005893125.1_ASM589312v1_genomic.fna/checkm_result
[2024-01-24 15:22:48,772] [INFO] Task succeeded: CheckM
[2024-01-24 15:22:48,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.45%
Strain heterogeneity: 63.64%
--------------------------------------------------------------------------------
[2024-01-24 15:22:48,804] [INFO] ===== Completeness check finished =====
[2024-01-24 15:22:48,804] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:22:48,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005893125.1_ASM589312v1_genomic.fna/markers.fasta)
[2024-01-24 15:22:48,805] [INFO] Task started: Blastn
[2024-01-24 15:22:48,805] [INFO] Running command: blastn -query GCF_005893125.1_ASM589312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga22f4cd7-579b-422c-a96d-2fc2aa9e1cb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_005893125.1_ASM589312v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:22:50,913] [INFO] Task succeeded: Blastn
[2024-01-24 15:22:50,918] [INFO] Selected 12 target genomes.
[2024-01-24 15:22:50,918] [INFO] Target genome list was writen to GCF_005893125.1_ASM589312v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:22:50,928] [INFO] Task started: fastANI
[2024-01-24 15:22:50,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg889c689f-0d52-4cce-abbe-cfee0f2c1f53/GCF_005893125.1_ASM589312v1_genomic.fna.gz --refList GCF_005893125.1_ASM589312v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005893125.1_ASM589312v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:23:32,366] [INFO] Task succeeded: fastANI
[2024-01-24 15:23:32,379] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:23:32,380] [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_005893125.1	s__Nonomuraea sp005893125	100.0	4441	4469	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_008065375.1	s__Nonomuraea sp008065375	88.4566	2720	4469	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	88.4498	2427	4469	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	88.1278	2656	4469	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	86.2776	2559	4469	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	86.2059	2442	4469	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	85.9863	2629	4469	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	85.6573	2158	4469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_006334985.2	s__Nonomuraea phyllanthi	85.344	2278	4469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_004348345.1	s__Nonomuraea longispora	85.1612	1895	4469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_000379885.1	s__Nonomuraea coxensis	85.1229	2053	4469	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	84.9864	2470	4469	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 15:23:32,381] [INFO] GTDB search result was written to GCF_005893125.1_ASM589312v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:23:32,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:23:32,393] [INFO] DFAST_QC result json was written to GCF_005893125.1_ASM589312v1_genomic.fna/dqc_result.json
[2024-01-24 15:23:32,393] [INFO] DFAST_QC completed!
[2024-01-24 15:23:32,393] [INFO] Total running time: 0h4m28s