[2024-01-25 20:17:20,660] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:20,662] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:20,662] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference
[2024-01-25 20:17:21,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:21,785] [INFO] Task started: Prodigal
[2024-01-25 20:17:21,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa6c704a-e96b-4073-a64d-2662f3b52ad3/GCF_003287285.1_ASM328728v1_genomic.fna.gz | prodigal -d GCF_003287285.1_ASM328728v1_genomic.fna/cds.fna -a GCF_003287285.1_ASM328728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:36,658] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:36,658] [INFO] Task started: HMMsearch
[2024-01-25 20:17:36,658] [INFO] Running command: hmmsearch --tblout GCF_003287285.1_ASM328728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/reference_markers.hmm GCF_003287285.1_ASM328728v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:36,930] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:36,931] [INFO] Found 6/6 markers.
[2024-01-25 20:17:36,973] [INFO] Query marker FASTA was written to GCF_003287285.1_ASM328728v1_genomic.fna/markers.fasta
[2024-01-25 20:17:36,973] [INFO] Task started: Blastn
[2024-01-25 20:17:36,973] [INFO] Running command: blastn -query GCF_003287285.1_ASM328728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/reference_markers.fasta -out GCF_003287285.1_ASM328728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:37,802] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:37,805] [INFO] Selected 20 target genomes.
[2024-01-25 20:17:37,806] [INFO] Target genome list was writen to GCF_003287285.1_ASM328728v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:37,821] [INFO] Task started: fastANI
[2024-01-25 20:17:37,822] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6c704a-e96b-4073-a64d-2662f3b52ad3/GCF_003287285.1_ASM328728v1_genomic.fna.gz --refList GCF_003287285.1_ASM328728v1_genomic.fna/target_genomes.txt --output GCF_003287285.1_ASM328728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:59,706] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:59,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:59,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:59,719] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:59,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:59,719] [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
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	100.0	1643	1645	95	conclusive
Phytoactinopolyspora halotolerans	strain=CCTCC AB 2017055	GCA_010550675.1	1981512	1981512	type	True	77.9493	589	1645	95	below_threshold
Phytoactinopolyspora mesophila	strain=XMNu-373	GCA_010122465.1	2650750	2650750	type	True	77.8834	516	1645	95	below_threshold
Haloactinopolyspora alba	strain=YIM 93246	GCA_004138525.1	648780	648780	type	True	77.8629	479	1645	95	below_threshold
Phytoactinopolyspora endophytica	strain=EGI 60009	GCA_004138495.1	1642495	1642495	type	True	77.8379	534	1645	95	below_threshold
Haloactinopolyspora alba	strain=DSM 45211	GCA_003014555.1	648780	648780	type	True	77.8276	482	1645	95	below_threshold
Phytoactinopolyspora alkaliphila	strain=CGMCC 4.7225	GCA_010550695.1	1783498	1783498	type	True	77.7812	482	1645	95	below_threshold
Phytoactinopolyspora limicola	strain=HAJB-30	GCA_011320225.1	2715536	2715536	type	True	77.7517	478	1645	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	77.5214	455	1645	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	77.4973	435	1645	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	77.4554	421	1645	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	77.4058	462	1645	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	77.2982	449	1645	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	77.2733	466	1645	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	77.2246	494	1645	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	76.1071	174	1645	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	75.9938	220	1645	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	75.8056	220	1645	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	75.7542	153	1645	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.66	298	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:59,725] [INFO] DFAST Taxonomy check result was written to GCF_003287285.1_ASM328728v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:59,726] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:59,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:59,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/checkm_data
[2024-01-25 20:17:59,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:59,774] [INFO] Task started: CheckM
[2024-01-25 20:17:59,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003287285.1_ASM328728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003287285.1_ASM328728v1_genomic.fna/checkm_input GCF_003287285.1_ASM328728v1_genomic.fna/checkm_result
[2024-01-25 20:18:47,094] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:47,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:47,113] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:47,113] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:47,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003287285.1_ASM328728v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:47,114] [INFO] Task started: Blastn
[2024-01-25 20:18:47,114] [INFO] Running command: blastn -query GCF_003287285.1_ASM328728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4eede3a-3e3b-42ac-a72f-8e7c085dfb4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003287285.1_ASM328728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:48,314] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:48,318] [INFO] Selected 17 target genomes.
[2024-01-25 20:18:48,319] [INFO] Target genome list was writen to GCF_003287285.1_ASM328728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:48,352] [INFO] Task started: fastANI
[2024-01-25 20:18:48,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa6c704a-e96b-4073-a64d-2662f3b52ad3/GCF_003287285.1_ASM328728v1_genomic.fna.gz --refList GCF_003287285.1_ASM328728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003287285.1_ASM328728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:08,410] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:08,421] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:08,422] [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_003287285.1	s__Phytoactinopolyspora halophila	100.0	1643	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010550675.1	s__Phytoactinopolyspora halotolerans	77.9551	588	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010122465.1	s__Phytoactinopolyspora mesophila	77.8765	517	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014555.1	s__Haloactinopolyspora alba	77.8269	482	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Haloactinopolyspora	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010550695.1	s__Phytoactinopolyspora alkaliphila	77.7641	486	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320225.1	s__Phytoactinopolyspora limicola	77.7315	481	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	77.543	452	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003579925.1	s__Jiangella rhizosphaerae	77.5026	435	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515395.1	s__Jiangella gansuensis	77.4353	424	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236295.1	s__Jiangella anatolica	77.3751	479	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349105.1	s__Jiangella aurantiaca	77.3737	467	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	77.3436	488	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001270745.1	s__Jiangella muralis	77.3027	462	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	77.2993	449	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106035.1	s__Jiangella alba	77.2726	483	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_003427025.1	s__Jiangella endophytica	77.2256	494	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188105.1	s__Spirillospora mexicana	75.6882	277	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:08,423] [INFO] GTDB search result was written to GCF_003287285.1_ASM328728v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:08,425] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:08,428] [INFO] DFAST_QC result json was written to GCF_003287285.1_ASM328728v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:08,429] [INFO] DFAST_QC completed!
[2024-01-25 20:19:08,429] [INFO] Total running time: 0h1m48s