[2024-01-24 13:54:03,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:03,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:03,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference
[2024-01-24 13:54:05,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,382] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,382] [INFO] Running command: gunzip -c /var/lib/cwl/stg733e237c-e3cd-4120-b815-b93fa07cdd51/GCF_014207985.1_ASM1420798v1_genomic.fna.gz | prodigal -d GCF_014207985.1_ASM1420798v1_genomic.fna/cds.fna -a GCF_014207985.1_ASM1420798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:45,061] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:45,062] [INFO] Task started: HMMsearch
[2024-01-24 13:54:45,062] [INFO] Running command: hmmsearch --tblout GCF_014207985.1_ASM1420798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/reference_markers.hmm GCF_014207985.1_ASM1420798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:45,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:45,569] [INFO] Found 6/6 markers.
[2024-01-24 13:54:45,671] [INFO] Query marker FASTA was written to GCF_014207985.1_ASM1420798v1_genomic.fna/markers.fasta
[2024-01-24 13:54:45,671] [INFO] Task started: Blastn
[2024-01-24 13:54:45,671] [INFO] Running command: blastn -query GCF_014207985.1_ASM1420798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/reference_markers.fasta -out GCF_014207985.1_ASM1420798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:47,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:47,127] [INFO] Selected 17 target genomes.
[2024-01-24 13:54:47,127] [INFO] Target genome list was writen to GCF_014207985.1_ASM1420798v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:47,154] [INFO] Task started: fastANI
[2024-01-24 13:54:47,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg733e237c-e3cd-4120-b815-b93fa07cdd51/GCF_014207985.1_ASM1420798v1_genomic.fna.gz --refList GCF_014207985.1_ASM1420798v1_genomic.fna/target_genomes.txt --output GCF_014207985.1_ASM1420798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:42,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:42,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:42,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:42,511] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:42,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:42,512] [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 rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	100.0	4292	4292	95	conclusive
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	88.1292	2703	4292	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	87.0278	2743	4292	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	86.6026	2894	4292	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	85.8782	2708	4292	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.8599	2698	4292	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.7081	2178	4292	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	85.6946	2225	4292	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.619	2515	4292	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.5473	2364	4292	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.5228	2511	4292	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.4994	2485	4292	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	85.4756	2533	4292	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.2281	2306	4292	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	85.1824	2251	4292	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.0787	1329	4292	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	82.9713	2115	4292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:42,513] [INFO] DFAST Taxonomy check result was written to GCF_014207985.1_ASM1420798v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:42,514] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:42,514] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:42,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/checkm_data
[2024-01-24 13:55:42,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:42,629] [INFO] Task started: CheckM
[2024-01-24 13:55:42,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207985.1_ASM1420798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207985.1_ASM1420798v1_genomic.fna/checkm_input GCF_014207985.1_ASM1420798v1_genomic.fna/checkm_result
[2024-01-24 13:58:36,767] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:36,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,799] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:36,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:36,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207985.1_ASM1420798v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:36,801] [INFO] Task started: Blastn
[2024-01-24 13:58:36,801] [INFO] Running command: blastn -query GCF_014207985.1_ASM1420798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb60a2f5b-fa96-4189-8832-de0224c3ab91/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207985.1_ASM1420798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:39,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:39,126] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:39,126] [INFO] Target genome list was writen to GCF_014207985.1_ASM1420798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:39,134] [INFO] Task started: fastANI
[2024-01-24 13:58:39,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg733e237c-e3cd-4120-b815-b93fa07cdd51/GCF_014207985.1_ASM1420798v1_genomic.fna.gz --refList GCF_014207985.1_ASM1420798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207985.1_ASM1420798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:20,127] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:20,141] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:20,141] [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_014207985.1	s__Nonomuraea rubra	100.0	4292	4292	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_008086045.1	s__Nonomuraea sp008086045	90.9154	3233	4292	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	90.0485	3184	4292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_000725485.1	s__Nonomuraea candida	88.118	2705	4292	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	87.0115	2747	4292	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	86.5724	2903	4292	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	85.8866	2689	4292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	85.717	2176	4292	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	85.6307	2512	4292	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	85.563	2359	4292	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	85.4217	2583	4292	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 13:59:20,143] [INFO] GTDB search result was written to GCF_014207985.1_ASM1420798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:20,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:20,147] [INFO] DFAST_QC result json was written to GCF_014207985.1_ASM1420798v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:20,147] [INFO] DFAST_QC completed!
[2024-01-24 13:59:20,147] [INFO] Total running time: 0h5m16s