[2024-01-24 12:23:03,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference
[2024-01-24 12:23:04,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:04,931] [INFO] Task started: Prodigal
[2024-01-24 12:23:04,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a3e228e-78cc-4353-a213-f42b393b87cd/GCF_005405885.1_ASM540588v1_genomic.fna.gz | prodigal -d GCF_005405885.1_ASM540588v1_genomic.fna/cds.fna -a GCF_005405885.1_ASM540588v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:23,076] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:23,077] [INFO] Task started: HMMsearch
[2024-01-24 12:23:23,077] [INFO] Running command: hmmsearch --tblout GCF_005405885.1_ASM540588v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/reference_markers.hmm GCF_005405885.1_ASM540588v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:23,395] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:23,397] [INFO] Found 6/6 markers.
[2024-01-24 12:23:23,449] [INFO] Query marker FASTA was written to GCF_005405885.1_ASM540588v1_genomic.fna/markers.fasta
[2024-01-24 12:23:23,450] [INFO] Task started: Blastn
[2024-01-24 12:23:23,450] [INFO] Running command: blastn -query GCF_005405885.1_ASM540588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/reference_markers.fasta -out GCF_005405885.1_ASM540588v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,818] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,823] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:24,823] [INFO] Target genome list was writen to GCF_005405885.1_ASM540588v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:24,832] [INFO] Task started: fastANI
[2024-01-24 12:23:24,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3e228e-78cc-4353-a213-f42b393b87cd/GCF_005405885.1_ASM540588v1_genomic.fna.gz --refList GCF_005405885.1_ASM540588v1_genomic.fna/target_genomes.txt --output GCF_005405885.1_ASM540588v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:00,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:00,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:00,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:00,197] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:00,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:00,197] [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
Saccharothrix coeruleofusca	strain=DSM 43679	GCA_017876325.1	33919	33919	type	True	79.839	941	1973	95	below_threshold
Saccharothrix coeruleofusca	strain=JCM 3313	GCA_014648515.1	33919	33919	type	True	79.7961	939	1973	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	79.6843	855	1973	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	79.6324	842	1973	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	79.3047	989	1973	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	79.2648	822	1973	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	79.1924	838	1973	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	79.12	825	1973	95	below_threshold
Saccharopolyspora hirsuta	strain=VKM Ac-666	GCA_008630535.1	1837	1837	type	True	79.087	849	1973	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	79.0816	910	1973	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	79.0657	1012	1973	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	79.0295	1029	1973	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	78.9396	927	1973	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	78.9392	939	1973	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	78.8845	760	1973	95	below_threshold
Amycolatopsis granulosa	strain=DSM 45669	GCA_011758745.1	185684	185684	type	True	78.8814	738	1973	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	78.7929	858	1973	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	78.6863	718	1973	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	78.6142	797	1973	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	78.5719	767	1973	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	78.561	801	1973	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	78.5057	789	1973	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	78.3681	806	1973	95	below_threshold
Pseudonocardia acaciae	strain=DSM 45401	GCA_000620785.1	551276	551276	type	True	78.0905	913	1973	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:00,200] [INFO] DFAST Taxonomy check result was written to GCF_005405885.1_ASM540588v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:00,200] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:00,200] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:00,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/checkm_data
[2024-01-24 12:24:00,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:00,258] [INFO] Task started: CheckM
[2024-01-24 12:24:00,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405885.1_ASM540588v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405885.1_ASM540588v1_genomic.fna/checkm_input GCF_005405885.1_ASM540588v1_genomic.fna/checkm_result
[2024-01-24 12:25:01,787] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:01,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:01,812] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:01,813] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:01,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405885.1_ASM540588v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:01,814] [INFO] Task started: Blastn
[2024-01-24 12:25:01,814] [INFO] Running command: blastn -query GCF_005405885.1_ASM540588v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b1933a5-70fb-4ed7-9948-0626f60c7465/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405885.1_ASM540588v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:03,816] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:03,819] [INFO] Selected 19 target genomes.
[2024-01-24 12:25:03,819] [INFO] Target genome list was writen to GCF_005405885.1_ASM540588v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:03,832] [INFO] Task started: fastANI
[2024-01-24 12:25:03,832] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a3e228e-78cc-4353-a213-f42b393b87cd/GCF_005405885.1_ASM540588v1_genomic.fna.gz --refList GCF_005405885.1_ASM540588v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405885.1_ASM540588v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:32,945] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:32,964] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:32,964] [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_005405885.1	s__Gandjariella thermophila	100.0	1968	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000715825.1	s__Goodfellowiella coeruleoviolacea	80.0643	1006	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Goodfellowiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648515.1	s__Actinosynnema coeruleofuscum	79.8743	923	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.37	99.37	0.97	0.97	2	-
GCF_900129375.1	s__Streptoalloteichus hindustanus	79.7444	846	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Streptoalloteichus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645795.1	s__Longimycelium tulufanense	79.6393	733	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Longimycelium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	79.4607	971	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410345.1	s__Saccharopolyspora hordei	79.2424	825	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	79.1128	903	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	79.0962	831	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_008630535.1	s__Saccharopolyspora hirsuta	79.0938	849	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	79.0869	1015	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004216555.1	s__Herbihabitans rhizosphaerae	79.0705	773	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Herbihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204915.1	s__Crossiella cryophila	78.9798	931	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Crossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	78.8418	768	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	78.686	717	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	78.5814	767	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	78.5392	783	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653945.1	s__Amycolatopsis deserti	78.486	865	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620785.1	s__Pseudonocardia acaciae	78.1065	908	1973	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:32,966] [INFO] GTDB search result was written to GCF_005405885.1_ASM540588v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:32,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:32,970] [INFO] DFAST_QC result json was written to GCF_005405885.1_ASM540588v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:32,971] [INFO] DFAST_QC completed!
[2024-01-24 12:25:32,971] [INFO] Total running time: 0h2m29s