[2024-01-24 10:47:40,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7a1716-0595-47e9-afca-2cf5f5e4cc00/GCF_019396385.1_ASM1939638v1_genomic.fna.gz | prodigal -d GCF_019396385.1_ASM1939638v1_genomic.fna/cds.fna -a GCF_019396385.1_ASM1939638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:10,250] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:10,250] [INFO] Task started: HMMsearch
[2024-01-24 10:48:10,251] [INFO] Running command: hmmsearch --tblout GCF_019396385.1_ASM1939638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/reference_markers.hmm GCF_019396385.1_ASM1939638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:10,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:10,654] [INFO] Found 6/6 markers.
[2024-01-24 10:48:10,729] [INFO] Query marker FASTA was written to GCF_019396385.1_ASM1939638v1_genomic.fna/markers.fasta
[2024-01-24 10:48:10,730] [INFO] Task started: Blastn
[2024-01-24 10:48:10,730] [INFO] Running command: blastn -query GCF_019396385.1_ASM1939638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/reference_markers.fasta -out GCF_019396385.1_ASM1939638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:12,148] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:12,153] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:12,153] [INFO] Target genome list was writen to GCF_019396385.1_ASM1939638v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:12,158] [INFO] Task started: fastANI
[2024-01-24 10:48:12,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7a1716-0595-47e9-afca-2cf5f5e4cc00/GCF_019396385.1_ASM1939638v1_genomic.fna.gz --refList GCF_019396385.1_ASM1939638v1_genomic.fna/target_genomes.txt --output GCF_019396385.1_ASM1939638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:57,017] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:57,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:57,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:57,038] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:57,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:57,038] [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 harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	100.0	3055	3061	95	conclusive
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	84.8782	1931	3061	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	84.6453	1939	3061	95	below_threshold
Nonomuraea glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	84.6411	1916	3061	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	83.9176	1769	3061	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.8948	1765	3061	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	83.6784	1924	3061	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	83.6344	1917	3061	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.5306	1170	3061	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.3273	1685	3061	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	83.3149	1791	3061	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.2497	1904	3061	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.1848	1773	3061	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	83.1625	1819	3061	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	82.9861	1783	3061	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	82.9707	1769	3061	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.914	1861	3061	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	82.835	1721	3061	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.8269	1839	3061	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:57,040] [INFO] DFAST Taxonomy check result was written to GCF_019396385.1_ASM1939638v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:57,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:57,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:57,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/checkm_data
[2024-01-24 10:48:57,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:57,126] [INFO] Task started: CheckM
[2024-01-24 10:48:57,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019396385.1_ASM1939638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019396385.1_ASM1939638v1_genomic.fna/checkm_input GCF_019396385.1_ASM1939638v1_genomic.fna/checkm_result
[2024-01-24 10:50:22,203] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:22,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.13%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:22,232] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:22,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:22,232] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019396385.1_ASM1939638v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:22,233] [INFO] Task started: Blastn
[2024-01-24 10:50:22,233] [INFO] Running command: blastn -query GCF_019396385.1_ASM1939638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc17f1435-2675-4172-9083-755c9a75c4e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019396385.1_ASM1939638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:24,509] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:24,513] [INFO] Selected 17 target genomes.
[2024-01-24 10:50:24,513] [INFO] Target genome list was writen to GCF_019396385.1_ASM1939638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:24,536] [INFO] Task started: fastANI
[2024-01-24 10:50:24,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7a1716-0595-47e9-afca-2cf5f5e4cc00/GCF_019396385.1_ASM1939638v1_genomic.fna.gz --refList GCF_019396385.1_ASM1939638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019396385.1_ASM1939638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:05,894] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:05,919] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:05,921] [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_008017515.1	s__Nonomuraea sp008017515	98.2261	2784	3061	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	85.2474	1904	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646515.1	s__Nonomuraea glycinis	84.6962	1905	3061	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	83.8919	1775	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379885.1	s__Nonomuraea coxensis	83.6622	1910	3061	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	83.343	1784	3061	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	83.3034	1689	3061	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	83.2359	1913	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	83.1969	1762	3061	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	83.1741	1817	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_004348995.1	s__Nonomuraea terrae	83.1044	1649	3061	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	82.9759	1786	3061	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	82.916	1860	3061	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	82.8369	1875	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109355.1	s__Nonomuraea pusilla	82.8245	1724	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.44	99.44	0.97	0.97	2	-
GCF_900108335.1	s__Nonomuraea solani	82.6799	1969	3061	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093975.1	s__Nonomuraea rubra_A	81.5832	1527	3061	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 10:51:05,923] [INFO] GTDB search result was written to GCF_019396385.1_ASM1939638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:05,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:05,928] [INFO] DFAST_QC result json was written to GCF_019396385.1_ASM1939638v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:05,929] [INFO] DFAST_QC completed!
[2024-01-24 10:51:05,929] [INFO] Total running time: 0h3m25s