[2024-01-24 15:02:23,230] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,232] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference
[2024-01-24 15:02:24,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,475] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg8045b2fa-9e7d-4688-9518-6a67c6a1f3db/GCF_014207745.1_ASM1420774v1_genomic.fna.gz | prodigal -d GCF_014207745.1_ASM1420774v1_genomic.fna/cds.fna -a GCF_014207745.1_ASM1420774v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:52,045] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:52,045] [INFO] Task started: HMMsearch
[2024-01-24 15:02:52,045] [INFO] Running command: hmmsearch --tblout GCF_014207745.1_ASM1420774v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/reference_markers.hmm GCF_014207745.1_ASM1420774v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:52,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:52,490] [INFO] Found 6/6 markers.
[2024-01-24 15:02:52,590] [INFO] Query marker FASTA was written to GCF_014207745.1_ASM1420774v1_genomic.fna/markers.fasta
[2024-01-24 15:02:52,590] [INFO] Task started: Blastn
[2024-01-24 15:02:52,590] [INFO] Running command: blastn -query GCF_014207745.1_ASM1420774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/reference_markers.fasta -out GCF_014207745.1_ASM1420774v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:54,074] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:54,078] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:54,078] [INFO] Target genome list was writen to GCF_014207745.1_ASM1420774v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:54,089] [INFO] Task started: fastANI
[2024-01-24 15:02:54,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg8045b2fa-9e7d-4688-9518-6a67c6a1f3db/GCF_014207745.1_ASM1420774v1_genomic.fna.gz --refList GCF_014207745.1_ASM1420774v1_genomic.fna/target_genomes.txt --output GCF_014207745.1_ASM1420774v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:33,550] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:33,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:33,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:33,562] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:33,562] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:33,562] [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 muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	100.0	3076	3076	95	conclusive
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	91.4069	2243	3076	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	86.8811	1518	3076	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	85.3871	2048	3076	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	85.3234	2028	3076	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.7763	1724	3076	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	84.726	1734	3076	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.9438	1202	3076	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	83.7054	2026	3076	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.581	1935	3076	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.487	1975	3076	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.2663	1855	3076	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	82.752	1637	3076	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.3824	1121	3076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,564] [INFO] DFAST Taxonomy check result was written to GCF_014207745.1_ASM1420774v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:33,568] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:33,568] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:33,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/checkm_data
[2024-01-24 15:03:33,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:33,705] [INFO] Task started: CheckM
[2024-01-24 15:03:33,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207745.1_ASM1420774v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207745.1_ASM1420774v1_genomic.fna/checkm_input GCF_014207745.1_ASM1420774v1_genomic.fna/checkm_result
[2024-01-24 15:05:23,255] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:23,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.13%
Strain heterogeneity: 62.50%
--------------------------------------------------------------------------------
[2024-01-24 15:05:23,286] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:23,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:23,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207745.1_ASM1420774v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:23,287] [INFO] Task started: Blastn
[2024-01-24 15:05:23,287] [INFO] Running command: blastn -query GCF_014207745.1_ASM1420774v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec396fa-5024-4d5a-b40a-14ea71ca6360/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207745.1_ASM1420774v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:25,553] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:25,557] [INFO] Selected 11 target genomes.
[2024-01-24 15:05:25,558] [INFO] Target genome list was writen to GCF_014207745.1_ASM1420774v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:25,567] [INFO] Task started: fastANI
[2024-01-24 15:05:25,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg8045b2fa-9e7d-4688-9518-6a67c6a1f3db/GCF_014207745.1_ASM1420774v1_genomic.fna.gz --refList GCF_014207745.1_ASM1420774v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207745.1_ASM1420774v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:57,119] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:57,137] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:57,137] [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_014207745.1	s__Nonomuraea muscovyensis	100.0	3076	3076	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_002850745.1	s__Nonomuraea indica	91.4421	2238	3076	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	85.3102	2031	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	85.274	2058	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	84.7889	1723	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	83.8183	1802	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603905.1	s__Nonomuraea sp018603905	83.7211	1967	3076	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	82.9659	1913	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	82.717	1643	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.5237	1835	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	79.3889	1119	3076	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:57,139] [INFO] GTDB search result was written to GCF_014207745.1_ASM1420774v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:57,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:57,143] [INFO] DFAST_QC result json was written to GCF_014207745.1_ASM1420774v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:57,143] [INFO] DFAST_QC completed!
[2024-01-24 15:05:57,143] [INFO] Total running time: 0h3m34s