[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference
[2024-01-24 12:00:39,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,381] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,381] [INFO] Running command: gunzip -c /var/lib/cwl/stge85a5f11-eab8-4957-8deb-926fbad15601/GCF_014646515.1_ASM1464651v1_genomic.fna.gz | prodigal -d GCF_014646515.1_ASM1464651v1_genomic.fna/cds.fna -a GCF_014646515.1_ASM1464651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:01:06,499] [INFO] Task succeeded: Prodigal
[2024-01-24 12:01:06,499] [INFO] Task started: HMMsearch
[2024-01-24 12:01:06,500] [INFO] Running command: hmmsearch --tblout GCF_014646515.1_ASM1464651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/reference_markers.hmm GCF_014646515.1_ASM1464651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:01:06,910] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:01:06,912] [INFO] Found 6/6 markers.
[2024-01-24 12:01:06,983] [INFO] Query marker FASTA was written to GCF_014646515.1_ASM1464651v1_genomic.fna/markers.fasta
[2024-01-24 12:01:06,984] [INFO] Task started: Blastn
[2024-01-24 12:01:06,984] [INFO] Running command: blastn -query GCF_014646515.1_ASM1464651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/reference_markers.fasta -out GCF_014646515.1_ASM1464651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:08,312] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:08,316] [INFO] Selected 17 target genomes.
[2024-01-24 12:01:08,317] [INFO] Target genome list was writen to GCF_014646515.1_ASM1464651v1_genomic.fna/target_genomes.txt
[2024-01-24 12:01:08,325] [INFO] Task started: fastANI
[2024-01-24 12:01:08,325] [INFO] Running command: fastANI --query /var/lib/cwl/stge85a5f11-eab8-4957-8deb-926fbad15601/GCF_014646515.1_ASM1464651v1_genomic.fna.gz --refList GCF_014646515.1_ASM1464651v1_genomic.fna/target_genomes.txt --output GCF_014646515.1_ASM1464651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:50,212] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:50,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:50,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:50,229] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:01:50,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:50,229] [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 glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	100.0	3187	3189	95	conclusive
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	99.9984	3181	3189	95	conclusive
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	84.6927	1957	3189	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	84.6113	1952	3189	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.0722	1688	3189	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	84.0492	1692	3189	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.7987	1159	3189	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.3676	1931	3189	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	83.3518	1797	3189	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	83.3205	1984	3189	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	83.1807	1965	3189	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	83.1092	1709	3189	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.0979	2036	3189	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.0758	1836	3189	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	82.9784	1897	3189	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	82.9768	2032	3189	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	82.8354	1818	3189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:50,232] [INFO] DFAST Taxonomy check result was written to GCF_014646515.1_ASM1464651v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:50,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:50,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:50,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/checkm_data
[2024-01-24 12:01:50,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:50,319] [INFO] Task started: CheckM
[2024-01-24 12:01:50,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646515.1_ASM1464651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646515.1_ASM1464651v1_genomic.fna/checkm_input GCF_014646515.1_ASM1464651v1_genomic.fna/checkm_result
[2024-01-24 12:03:13,863] [INFO] Task succeeded: CheckM
[2024-01-24 12:03:13,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:03:13,896] [INFO] ===== Completeness check finished =====
[2024-01-24 12:03:13,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:03:13,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646515.1_ASM1464651v1_genomic.fna/markers.fasta)
[2024-01-24 12:03:13,897] [INFO] Task started: Blastn
[2024-01-24 12:03:13,897] [INFO] Running command: blastn -query GCF_014646515.1_ASM1464651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3bfcb42d-b7eb-4c27-ba65-d8afb5a90273/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646515.1_ASM1464651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:03:15,998] [INFO] Task succeeded: Blastn
[2024-01-24 12:03:16,006] [INFO] Selected 18 target genomes.
[2024-01-24 12:03:16,006] [INFO] Target genome list was writen to GCF_014646515.1_ASM1464651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:03:16,022] [INFO] Task started: fastANI
[2024-01-24 12:03:16,022] [INFO] Running command: fastANI --query /var/lib/cwl/stge85a5f11-eab8-4957-8deb-926fbad15601/GCF_014646515.1_ASM1464651v1_genomic.fna.gz --refList GCF_014646515.1_ASM1464651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646515.1_ASM1464651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:04:00,427] [INFO] Task succeeded: fastANI
[2024-01-24 12:04:00,454] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:04:00,454] [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_014646515.1	s__Nonomuraea glycinis	100.0	3187	3189	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_001083785.1	s__Nonomuraea sp001083785	85.3471	1904	3189	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	84.7235	1966	3189	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	84.0306	1696	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362835.1	s__Nonomuraea sp013362835	83.9684	862	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	83.3656	1796	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	83.3223	1700	3189	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	83.1699	1969	3189	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	83.1315	1706	3189	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	83.1132	2033	3189	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	83.0196	2021	3189	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	82.9745	1803	3189	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	82.9521	2014	3189	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	82.8784	1895	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	82.7708	1832	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_008086045.1	s__Nonomuraea sp008086045	82.7542	1961	3189	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	82.7336	2020	3189	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.1417	1725	3189	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 12:04:00,456] [INFO] GTDB search result was written to GCF_014646515.1_ASM1464651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:04:00,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:04:00,461] [INFO] DFAST_QC result json was written to GCF_014646515.1_ASM1464651v1_genomic.fna/dqc_result.json
[2024-01-24 12:04:00,462] [INFO] DFAST_QC completed!
[2024-01-24 12:04:00,462] [INFO] Total running time: 0h3m24s