[2024-01-25 18:04:50,624] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:04:50,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:04:50,626] [INFO] DQC Reference Directory: /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference
[2024-01-25 18:04:51,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:04:51,766] [INFO] Task started: Prodigal
[2024-01-25 18:04:51,766] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9c8eae0-256c-470b-ab88-a3a0074b5192/GCF_016863415.1_ASM1686341v1_genomic.fna.gz | prodigal -d GCF_016863415.1_ASM1686341v1_genomic.fna/cds.fna -a GCF_016863415.1_ASM1686341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:12,161] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:12,161] [INFO] Task started: HMMsearch
[2024-01-25 18:05:12,161] [INFO] Running command: hmmsearch --tblout GCF_016863415.1_ASM1686341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/reference_markers.hmm GCF_016863415.1_ASM1686341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:12,475] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:12,476] [INFO] Found 6/6 markers.
[2024-01-25 18:05:12,539] [INFO] Query marker FASTA was written to GCF_016863415.1_ASM1686341v1_genomic.fna/markers.fasta
[2024-01-25 18:05:12,539] [INFO] Task started: Blastn
[2024-01-25 18:05:12,539] [INFO] Running command: blastn -query GCF_016863415.1_ASM1686341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/reference_markers.fasta -out GCF_016863415.1_ASM1686341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:13,793] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:13,795] [INFO] Selected 11 target genomes.
[2024-01-25 18:05:13,796] [INFO] Target genome list was writen to GCF_016863415.1_ASM1686341v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:13,798] [INFO] Task started: fastANI
[2024-01-25 18:05:13,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c8eae0-256c-470b-ab88-a3a0074b5192/GCF_016863415.1_ASM1686341v1_genomic.fna.gz --refList GCF_016863415.1_ASM1686341v1_genomic.fna/target_genomes.txt --output GCF_016863415.1_ASM1686341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:37,966] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:37,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:37,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:37,975] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:05:37,975] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:05:37,975] [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
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	100.0	2775	2777	95	conclusive
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	99.9997	2776	2777	95	conclusive
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	94.5886	2395	2777	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	94.5859	2373	2777	95	below_threshold
Sphaerisporangium album	strain=CCTCC AA 208026	GCA_003323745.1	509200	509200	type	True	86.2093	1799	2777	95	below_threshold
Sphaerisporangium corydalis	strain=NEAU-YHS15	GCA_025506355.1	1441875	1441875	type	True	83.1	1562	2777	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	82.8351	1501	2777	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.7153	1333	2777	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.6158	858	2777	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	79.3887	1287	2777	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	79.3355	1276	2777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:37,976] [INFO] DFAST Taxonomy check result was written to GCF_016863415.1_ASM1686341v1_genomic.fna/tc_result.tsv
[2024-01-25 18:05:37,977] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:37,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:37,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/checkm_data
[2024-01-25 18:05:37,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:38,059] [INFO] Task started: CheckM
[2024-01-25 18:05:38,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016863415.1_ASM1686341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016863415.1_ASM1686341v1_genomic.fna/checkm_input GCF_016863415.1_ASM1686341v1_genomic.fna/checkm_result
[2024-01-25 18:06:56,607] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:56,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 9.38%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2024-01-25 18:06:56,634] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:56,634] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:56,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016863415.1_ASM1686341v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:56,635] [INFO] Task started: Blastn
[2024-01-25 18:06:56,635] [INFO] Running command: blastn -query GCF_016863415.1_ASM1686341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafad542b-38e8-4608-b5ef-1534dd22500b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016863415.1_ASM1686341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:58,703] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:58,706] [INFO] Selected 8 target genomes.
[2024-01-25 18:06:58,706] [INFO] Target genome list was writen to GCF_016863415.1_ASM1686341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:58,709] [INFO] Task started: fastANI
[2024-01-25 18:06:58,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c8eae0-256c-470b-ab88-a3a0074b5192/GCF_016863415.1_ASM1686341v1_genomic.fna.gz --refList GCF_016863415.1_ASM1686341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016863415.1_ASM1686341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:16,486] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:16,492] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:16,492] [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_014205275.1	s__Sphaerisporangium siamense	99.9997	2776	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014200435.1	s__Sphaerisporangium krabiense	94.5972	2394	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003323745.1	s__Sphaerisporangium album	86.1632	1805	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	82.7926	1509	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_018531465.1	s__Sphaerisporangium sp018531465	82.751	1620	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863395.1	s__Sphaerisporangium rufum	81.951	1393	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113865.1	s__Streptosporangium canum	80.0898	1340	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCA_014647935.1	s__Planomonospora parontospora	79.8693	1217	2777	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora	95.0	97.40	95.90	0.89	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:16,493] [INFO] GTDB search result was written to GCF_016863415.1_ASM1686341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:16,494] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:16,499] [INFO] DFAST_QC result json was written to GCF_016863415.1_ASM1686341v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:16,500] [INFO] DFAST_QC completed!
[2024-01-25 18:07:16,500] [INFO] Total running time: 0h2m26s