[2024-01-24 13:46:43,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:43,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:43,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference
[2024-01-24 13:46:45,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:45,281] [INFO] Task started: Prodigal
[2024-01-24 13:46:45,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c3805bd-a2a0-40c4-9371-2a8183e383de/GCF_020682705.1_ASM2068270v1_genomic.fna.gz | prodigal -d GCF_020682705.1_ASM2068270v1_genomic.fna/cds.fna -a GCF_020682705.1_ASM2068270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:57,054] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:57,054] [INFO] Task started: HMMsearch
[2024-01-24 13:46:57,054] [INFO] Running command: hmmsearch --tblout GCF_020682705.1_ASM2068270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/reference_markers.hmm GCF_020682705.1_ASM2068270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:57,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:57,367] [INFO] Found 6/6 markers.
[2024-01-24 13:46:57,401] [INFO] Query marker FASTA was written to GCF_020682705.1_ASM2068270v1_genomic.fna/markers.fasta
[2024-01-24 13:46:57,402] [INFO] Task started: Blastn
[2024-01-24 13:46:57,402] [INFO] Running command: blastn -query GCF_020682705.1_ASM2068270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/reference_markers.fasta -out GCF_020682705.1_ASM2068270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:58,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:58,498] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:58,499] [INFO] Target genome list was writen to GCF_020682705.1_ASM2068270v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:58,506] [INFO] Task started: fastANI
[2024-01-24 13:46:58,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3805bd-a2a0-40c4-9371-2a8183e383de/GCF_020682705.1_ASM2068270v1_genomic.fna.gz --refList GCF_020682705.1_ASM2068270v1_genomic.fna/target_genomes.txt --output GCF_020682705.1_ASM2068270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:09,849] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:09,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:09,861] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:47:09,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:47:09,861] [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
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	82.7211	796	1330	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	82.6298	779	1330	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	82.6028	800	1330	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	82.5888	754	1330	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	82.5589	819	1330	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.4323	737	1330	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	82.3926	780	1330	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	82.3099	794	1330	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	82.2843	726	1330	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	82.1347	778	1330	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	81.9838	721	1330	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	81.6079	742	1330	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.4177	590	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,863] [INFO] DFAST Taxonomy check result was written to GCF_020682705.1_ASM2068270v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:09,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:09,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:09,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/checkm_data
[2024-01-24 13:47:09,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:09,909] [INFO] Task started: CheckM
[2024-01-24 13:47:09,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020682705.1_ASM2068270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020682705.1_ASM2068270v1_genomic.fna/checkm_input GCF_020682705.1_ASM2068270v1_genomic.fna/checkm_result
[2024-01-24 13:48:11,950] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:11,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:11,972] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:11,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:11,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020682705.1_ASM2068270v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:11,973] [INFO] Task started: Blastn
[2024-01-24 13:48:11,973] [INFO] Running command: blastn -query GCF_020682705.1_ASM2068270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d1b381-8e48-4db9-b8c2-a3af9f30f919/dqc_reference/reference_markers_gtdb.fasta -out GCF_020682705.1_ASM2068270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:13,651] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:13,655] [INFO] Selected 23 target genomes.
[2024-01-24 13:48:13,655] [INFO] Target genome list was writen to GCF_020682705.1_ASM2068270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:13,687] [INFO] Task started: fastANI
[2024-01-24 13:48:13,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c3805bd-a2a0-40c4-9371-2a8183e383de/GCF_020682705.1_ASM2068270v1_genomic.fna.gz --refList GCF_020682705.1_ASM2068270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020682705.1_ASM2068270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:34,329] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:34,350] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:48:34,351] [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_001422925.1	s__Microbacterium sp001422925	82.7453	836	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277855.1	s__Microbacterium sp015277855	82.702	798	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278255.1	s__Microbacterium hibisci	82.6633	775	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010634855.1	s__Microbacterium sp010634855	82.6502	799	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCF_003999995.1	s__Microbacterium sp003999995	82.6449	748	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386735.1	s__Microbacterium trichothecenolyticum_A	82.5934	839	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010105.1	s__Microbacterium sp004010105	82.5914	522	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278315.1	s__Microbacterium ureisolvens	82.5855	802	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	82.5347	820	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837165.1	s__Microbacterium sp014837165	82.4614	735	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779795.1	s__Microbacterium helvum	82.3582	783	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380605.1	s__Microbacterium sp000380605	82.3547	787	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427145.1	s__Microbacterium sp001427145	82.3246	724	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015278355.1	s__Microbacterium yannicii_B	82.3236	807	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	82.274	727	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524205.1	s__Microbacterium sp012524205	82.2008	778	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006783905.1	s__Microbacterium kyungheense	82.1604	775	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428485.1	s__Microbacterium sp001428485	82.1037	713	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	81.9206	737	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_012847295.1	s__Microbacterium sp012847295	81.8024	693	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907635.1	s__Microbacterium insulae	81.708	687	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900292075.1	s__Microbacterium timonense	81.5981	743	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362195.1	s__Microbacterium sp004362195	80.6101	627	1330	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:34,352] [INFO] GTDB search result was written to GCF_020682705.1_ASM2068270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:34,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:34,357] [INFO] DFAST_QC result json was written to GCF_020682705.1_ASM2068270v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:34,357] [INFO] DFAST_QC completed!
[2024-01-24 13:48:34,357] [INFO] Total running time: 0h1m50s