[2024-01-24 15:27:12,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference
[2024-01-24 15:27:13,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:13,898] [INFO] Task started: Prodigal
[2024-01-24 15:27:13,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg1879c0f0-ebb8-419d-bbd7-456a404b0bb3/GCF_014204795.1_ASM1420479v1_genomic.fna.gz | prodigal -d GCF_014204795.1_ASM1420479v1_genomic.fna/cds.fna -a GCF_014204795.1_ASM1420479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:57,955] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:57,955] [INFO] Task started: HMMsearch
[2024-01-24 15:27:57,955] [INFO] Running command: hmmsearch --tblout GCF_014204795.1_ASM1420479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/reference_markers.hmm GCF_014204795.1_ASM1420479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:58,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:58,503] [INFO] Found 6/6 markers.
[2024-01-24 15:27:58,603] [INFO] Query marker FASTA was written to GCF_014204795.1_ASM1420479v1_genomic.fna/markers.fasta
[2024-01-24 15:27:58,604] [INFO] Task started: Blastn
[2024-01-24 15:27:58,604] [INFO] Running command: blastn -query GCF_014204795.1_ASM1420479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/reference_markers.fasta -out GCF_014204795.1_ASM1420479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:00,007] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:00,011] [INFO] Selected 17 target genomes.
[2024-01-24 15:28:00,012] [INFO] Target genome list was writen to GCF_014204795.1_ASM1420479v1_genomic.fna/target_genomes.txt
[2024-01-24 15:28:00,024] [INFO] Task started: fastANI
[2024-01-24 15:28:00,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg1879c0f0-ebb8-419d-bbd7-456a404b0bb3/GCF_014204795.1_ASM1420479v1_genomic.fna.gz --refList GCF_014204795.1_ASM1420479v1_genomic.fna/target_genomes.txt --output GCF_014204795.1_ASM1420479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:55,586] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:55,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:55,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:55,607] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:55,607] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:55,607] [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 jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	100.0	4391	4391	95	conclusive
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	94.9032	3571	4391	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	87.5825	2541	4391	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	87.4558	2533	4391	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	86.4103	2590	4391	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	86.3722	2591	4391	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	86.1493	2340	4391	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	86.0045	2605	4391	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.9805	2809	4391	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.8855	2719	4391	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.8018	2202	4391	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.4094	2563	4391	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.0743	2012	4391	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.4237	2369	4391	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.1877	1323	4391	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	83.39	2176	4391	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.3875	2176	4391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:55,610] [INFO] DFAST Taxonomy check result was written to GCF_014204795.1_ASM1420479v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:55,610] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:55,610] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:55,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/checkm_data
[2024-01-24 15:28:55,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:55,727] [INFO] Task started: CheckM
[2024-01-24 15:28:55,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014204795.1_ASM1420479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014204795.1_ASM1420479v1_genomic.fna/checkm_input GCF_014204795.1_ASM1420479v1_genomic.fna/checkm_result
[2024-01-24 15:31:55,359] [INFO] Task succeeded: CheckM
[2024-01-24 15:31:55,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.30%
Strain heterogeneity: 44.44%
--------------------------------------------------------------------------------
[2024-01-24 15:31:55,396] [INFO] ===== Completeness check finished =====
[2024-01-24 15:31:55,396] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:31:55,397] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014204795.1_ASM1420479v1_genomic.fna/markers.fasta)
[2024-01-24 15:31:55,397] [INFO] Task started: Blastn
[2024-01-24 15:31:55,397] [INFO] Running command: blastn -query GCF_014204795.1_ASM1420479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5391cf0b-3b4b-4a76-9566-0909ba81e5e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014204795.1_ASM1420479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:31:57,462] [INFO] Task succeeded: Blastn
[2024-01-24 15:31:57,467] [INFO] Selected 14 target genomes.
[2024-01-24 15:31:57,467] [INFO] Target genome list was writen to GCF_014204795.1_ASM1420479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:31:57,478] [INFO] Task started: fastANI
[2024-01-24 15:31:57,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg1879c0f0-ebb8-419d-bbd7-456a404b0bb3/GCF_014204795.1_ASM1420479v1_genomic.fna.gz --refList GCF_014204795.1_ASM1420479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014204795.1_ASM1420479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:32:45,374] [INFO] Task succeeded: fastANI
[2024-01-24 15:32:45,389] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:32:45,389] [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_014204795.1	s__Nonomuraea jabiensis	100.0	4390	4391	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_014873145.1	s__Nonomuraea angiospora	94.886	3575	4391	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	87.4711	2528	4391	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	86.4381	2585	4391	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	86.3658	2590	4391	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	86.1527	2339	4391	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	86.0845	2594	4391	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	86.0085	2802	4391	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	86.001	2610	4391	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	85.8231	2736	4391	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	85.3279	2612	4391	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	85.1058	2006	4391	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	85.0517	2052	4391	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	83.4143	2172	4391	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 15:32:45,391] [INFO] GTDB search result was written to GCF_014204795.1_ASM1420479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:32:45,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:32:45,395] [INFO] DFAST_QC result json was written to GCF_014204795.1_ASM1420479v1_genomic.fna/dqc_result.json
[2024-01-24 15:32:45,396] [INFO] DFAST_QC completed!
[2024-01-24 15:32:45,396] [INFO] Total running time: 0h5m33s