[2024-01-24 13:31:35,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:35,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:35,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference
[2024-01-24 13:31:36,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:36,643] [INFO] Task started: Prodigal
[2024-01-24 13:31:36,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg75ff53f7-71cd-4fb1-a75d-3dda6e673c81/GCF_007992455.1_ASM799245v1_genomic.fna.gz | prodigal -d GCF_007992455.1_ASM799245v1_genomic.fna/cds.fna -a GCF_007992455.1_ASM799245v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:44,923] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:44,923] [INFO] Task started: HMMsearch
[2024-01-24 13:31:44,923] [INFO] Running command: hmmsearch --tblout GCF_007992455.1_ASM799245v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/reference_markers.hmm GCF_007992455.1_ASM799245v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:45,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:45,242] [INFO] Found 6/6 markers.
[2024-01-24 13:31:45,276] [INFO] Query marker FASTA was written to GCF_007992455.1_ASM799245v1_genomic.fna/markers.fasta
[2024-01-24 13:31:45,277] [INFO] Task started: Blastn
[2024-01-24 13:31:45,277] [INFO] Running command: blastn -query GCF_007992455.1_ASM799245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/reference_markers.fasta -out GCF_007992455.1_ASM799245v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:46,553] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:46,556] [INFO] Selected 21 target genomes.
[2024-01-24 13:31:46,556] [INFO] Target genome list was writen to GCF_007992455.1_ASM799245v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:46,565] [INFO] Task started: fastANI
[2024-01-24 13:31:46,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg75ff53f7-71cd-4fb1-a75d-3dda6e673c81/GCF_007992455.1_ASM799245v1_genomic.fna.gz --refList GCF_007992455.1_ASM799245v1_genomic.fna/target_genomes.txt --output GCF_007992455.1_ASM799245v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,579] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:04,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:04,580] [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 saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	100.0	977	982	95	conclusive
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	99.9999	982	982	95	conclusive
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	82.3111	617	982	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	81.9423	607	982	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	81.9192	622	982	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	81.8859	616	982	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.5431	576	982	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	81.197	567	982	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	81.1677	540	982	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	81.118	586	982	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	81.0848	562	982	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.0811	572	982	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	81.0387	592	982	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	81.032	586	982	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.9736	588	982	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.9444	592	982	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.9297	581	982	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.7005	593	982	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	80.696	517	982	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	79.8556	481	982	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	79.8482	462	982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,592] [INFO] DFAST Taxonomy check result was written to GCF_007992455.1_ASM799245v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,593] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/checkm_data
[2024-01-24 13:32:04,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,639] [INFO] Task started: CheckM
[2024-01-24 13:32:04,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007992455.1_ASM799245v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007992455.1_ASM799245v1_genomic.fna/checkm_input GCF_007992455.1_ASM799245v1_genomic.fna/checkm_result
[2024-01-24 13:32:46,078] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:46,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:46,093] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:46,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:46,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007992455.1_ASM799245v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:46,095] [INFO] Task started: Blastn
[2024-01-24 13:32:46,095] [INFO] Running command: blastn -query GCF_007992455.1_ASM799245v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f859520-b227-42cf-b93f-7bde114fd362/dqc_reference/reference_markers_gtdb.fasta -out GCF_007992455.1_ASM799245v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,264] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:48,264] [INFO] Target genome list was writen to GCF_007992455.1_ASM799245v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:48,279] [INFO] Task started: fastANI
[2024-01-24 13:32:48,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg75ff53f7-71cd-4fb1-a75d-3dda6e673c81/GCF_007992455.1_ASM799245v1_genomic.fna.gz --refList GCF_007992455.1_ASM799245v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007992455.1_ASM799245v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:02,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,985] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:02,986] [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_007992455.1	s__Microbacterium saccharophilum	100.0	977	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.54	98.03	0.93	0.90	5	conclusive
GCA_900078385.1	s__Microbacterium sp900078385	89.4825	782	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807485.1	s__Microbacterium sp016807485	82.298	411	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651225.1	s__Microbacterium telephonicum	82.2524	621	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898315.1	s__Microbacterium sp001898315	82.173	603	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001592125.1	s__Microbacterium hominis	81.9746	604	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCA_014197265.1	s__Microbacterium invictum	81.9341	633	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007828185.1	s__Microbacterium sp007828185	81.6965	579	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305435.1	s__Microbacterium sp017305435	81.6305	594	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314225.1	s__Microbacterium sp001314225	81.506	565	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644225.1	s__Microbacterium oleivorans_A	81.4605	587	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102005.1	s__Microbacterium sp900102005	81.2133	548	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.39	98.39	0.95	0.95	2	-
GCF_001691565.1	s__Microbacterium oleivorans_B	81.176	528	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	81.1166	617	982	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	81.0806	572	982	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	81.05	565	982	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	80.9262	593	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427525.1	s__Microbacterium sp001427525	80.7916	544	982	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409015.1	s__Microbacterium sp013409015	80.7046	545	982	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 13:33:02,987] [INFO] GTDB search result was written to GCF_007992455.1_ASM799245v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:02,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:02,992] [INFO] DFAST_QC result json was written to GCF_007992455.1_ASM799245v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:02,992] [INFO] DFAST_QC completed!
[2024-01-24 13:33:02,992] [INFO] Total running time: 0h1m28s