[2024-01-24 12:06:13,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,296] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,297] [INFO] DQC Reference Directory: /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference
[2024-01-24 12:06:14,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,723] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,723] [INFO] Running command: gunzip -c /var/lib/cwl/stgfefd7dd5-8ad9-4734-a4bd-e6ad6a9904e6/GCF_005889725.1_ASM588972v1_genomic.fna.gz | prodigal -d GCF_005889725.1_ASM588972v1_genomic.fna/cds.fna -a GCF_005889725.1_ASM588972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:53,437] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:53,438] [INFO] Task started: HMMsearch
[2024-01-24 12:06:53,438] [INFO] Running command: hmmsearch --tblout GCF_005889725.1_ASM588972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/reference_markers.hmm GCF_005889725.1_ASM588972v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:54,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:54,121] [INFO] Found 6/6 markers.
[2024-01-24 12:06:54,229] [INFO] Query marker FASTA was written to GCF_005889725.1_ASM588972v1_genomic.fna/markers.fasta
[2024-01-24 12:06:54,230] [INFO] Task started: Blastn
[2024-01-24 12:06:54,230] [INFO] Running command: blastn -query GCF_005889725.1_ASM588972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/reference_markers.fasta -out GCF_005889725.1_ASM588972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:55,608] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:55,613] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:55,613] [INFO] Target genome list was writen to GCF_005889725.1_ASM588972v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:55,662] [INFO] Task started: fastANI
[2024-01-24 12:06:55,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgfefd7dd5-8ad9-4734-a4bd-e6ad6a9904e6/GCF_005889725.1_ASM588972v1_genomic.fna.gz --refList GCF_005889725.1_ASM588972v1_genomic.fna/target_genomes.txt --output GCF_005889725.1_ASM588972v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:52,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:52,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:52,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:52,663] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:52,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:52,664] [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 zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	100.0	4125	4156	95	conclusive
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	86.3342	2670	4156	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	86.2751	2621	4156	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	86.2557	2633	4156	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	86.1207	2443	4156	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.8599	2241	4156	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.7899	2354	4156	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.7877	2336	4156	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	85.7482	2392	4156	95	below_threshold
Nonomuraea jiangxiensis	strain=CGMCC 4.6533	GCA_900099965.1	633440	633440	type	True	85.6637	2406	4156	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.589	2366	4156	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.5065	2554	4156	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	85.3898	2102	4156	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.5387	2334	4156	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.1551	1306	4156	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.4606	2286	4156	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.4366	1813	4156	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	83.1121	1400	4156	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	82.7728	1959	4156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:52,666] [INFO] DFAST Taxonomy check result was written to GCF_005889725.1_ASM588972v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:52,666] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:52,666] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:52,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/checkm_data
[2024-01-24 12:07:52,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:52,786] [INFO] Task started: CheckM
[2024-01-24 12:07:52,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005889725.1_ASM588972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005889725.1_ASM588972v1_genomic.fna/checkm_input GCF_005889725.1_ASM588972v1_genomic.fna/checkm_result
[2024-01-24 12:09:47,077] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:47,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 11.69%
Strain heterogeneity: 62.50%
--------------------------------------------------------------------------------
[2024-01-24 12:09:47,118] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:47,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:47,119] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005889725.1_ASM588972v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:47,119] [INFO] Task started: Blastn
[2024-01-24 12:09:47,119] [INFO] Running command: blastn -query GCF_005889725.1_ASM588972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2779f899-8794-46e6-bdc5-96abd600de15/dqc_reference/reference_markers_gtdb.fasta -out GCF_005889725.1_ASM588972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:49,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:49,157] [INFO] Selected 17 target genomes.
[2024-01-24 12:09:49,158] [INFO] Target genome list was writen to GCF_005889725.1_ASM588972v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:49,726] [INFO] Task started: fastANI
[2024-01-24 12:09:49,728] [INFO] Running command: fastANI --query /var/lib/cwl/stgfefd7dd5-8ad9-4734-a4bd-e6ad6a9904e6/GCF_005889725.1_ASM588972v1_genomic.fna.gz --refList GCF_005889725.1_ASM588972v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005889725.1_ASM588972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:43,629] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:43,649] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:43,649] [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_005889725.1	s__Nonomuraea zeae	100.0	4125	4156	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_900108335.1	s__Nonomuraea solani	86.3329	2671	4156	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	86.2901	2617	4156	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	86.2286	2640	4156	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	86.0905	2449	4156	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	85.8893	2155	4156	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	85.8868	2690	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	85.7849	2384	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	85.7041	2399	4156	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	85.6474	2758	4156	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	85.5637	2373	4156	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	85.552	2382	4156	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	85.5506	2544	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	85.2788	2674	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014648435.1	s__Nonomuraea spiralis	84.5042	2346	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_014646355.1	s__Nonomuraea cavernae	83.396	1818	4156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	82.7624	1975	4156	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 12:10:43,651] [INFO] GTDB search result was written to GCF_005889725.1_ASM588972v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:43,652] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:43,657] [INFO] DFAST_QC result json was written to GCF_005889725.1_ASM588972v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:43,657] [INFO] DFAST_QC completed!
[2024-01-24 12:10:43,657] [INFO] Total running time: 0h4m30s