[2024-01-24 11:52:04,788] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:52:04,790] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:52:04,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference
[2024-01-24 11:52:05,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:52:05,992] [INFO] Task started: Prodigal
[2024-01-24 11:52:05,992] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2a7f196-f040-4a41-a078-71084c0a1cf1/GCF_028737425.1_ASM2873742v1_genomic.fna.gz | prodigal -d GCF_028737425.1_ASM2873742v1_genomic.fna/cds.fna -a GCF_028737425.1_ASM2873742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:14,862] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:14,863] [INFO] Task started: HMMsearch
[2024-01-24 11:52:14,863] [INFO] Running command: hmmsearch --tblout GCF_028737425.1_ASM2873742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/reference_markers.hmm GCF_028737425.1_ASM2873742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:15,120] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:15,122] [INFO] Found 6/6 markers.
[2024-01-24 11:52:15,154] [INFO] Query marker FASTA was written to GCF_028737425.1_ASM2873742v1_genomic.fna/markers.fasta
[2024-01-24 11:52:15,154] [INFO] Task started: Blastn
[2024-01-24 11:52:15,154] [INFO] Running command: blastn -query GCF_028737425.1_ASM2873742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/reference_markers.fasta -out GCF_028737425.1_ASM2873742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:16,370] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:16,374] [INFO] Selected 23 target genomes.
[2024-01-24 11:52:16,375] [INFO] Target genome list was writen to GCF_028737425.1_ASM2873742v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:16,416] [INFO] Task started: fastANI
[2024-01-24 11:52:16,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a7f196-f040-4a41-a078-71084c0a1cf1/GCF_028737425.1_ASM2873742v1_genomic.fna.gz --refList GCF_028737425.1_ASM2873742v1_genomic.fna/target_genomes.txt --output GCF_028737425.1_ASM2873742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:31,457] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:31,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:31,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:31,478] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:31,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:31,479] [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 imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	85.7277	803	1068	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	84.0139	758	1068	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.3126	560	1068	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.1288	522	1068	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.099	549	1068	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.0589	538	1068	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.9157	548	1068	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	80.8773	531	1068	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.7673	519	1068	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.744	519	1068	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	80.7143	525	1068	95	below_threshold
Microbacterium oleivorans	strain=NBRC 103075	GCA_001552475.1	273677	273677	suspected-type	True	80.7057	511	1068	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.614	492	1068	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.6132	546	1068	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.6076	552	1068	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.5967	512	1068	95	below_threshold
Microbacterium flavum	strain=DSM 18909	GCA_018717645.1	415216	415216	type	True	80.582	502	1068	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.5187	534	1068	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	80.3957	537	1068	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	80.3955	537	1068	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.2267	514	1068	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.2138	512	1068	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.0575	523	1068	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,481] [INFO] DFAST Taxonomy check result was written to GCF_028737425.1_ASM2873742v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:31,482] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:31,482] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:31,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/checkm_data
[2024-01-24 11:52:31,483] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:31,522] [INFO] Task started: CheckM
[2024-01-24 11:52:31,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028737425.1_ASM2873742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028737425.1_ASM2873742v1_genomic.fna/checkm_input GCF_028737425.1_ASM2873742v1_genomic.fna/checkm_result
[2024-01-24 11:53:16,543] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:16,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:16,565] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:16,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:16,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028737425.1_ASM2873742v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:16,566] [INFO] Task started: Blastn
[2024-01-24 11:53:16,566] [INFO] Running command: blastn -query GCF_028737425.1_ASM2873742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg241d2fce-9b8b-446a-ad6a-973227937d66/dqc_reference/reference_markers_gtdb.fasta -out GCF_028737425.1_ASM2873742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:18,503] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:18,507] [INFO] Selected 6 target genomes.
[2024-01-24 11:53:18,508] [INFO] Target genome list was writen to GCF_028737425.1_ASM2873742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:18,512] [INFO] Task started: fastANI
[2024-01-24 11:53:18,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2a7f196-f040-4a41-a078-71084c0a1cf1/GCF_028737425.1_ASM2873742v1_genomic.fna.gz --refList GCF_028737425.1_ASM2873742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028737425.1_ASM2873742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:23,723] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:23,735] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:23,735] [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_003289625.1	s__Microbacterium sp003289625	97.6443	985	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	conclusive
GCF_002245215.1	s__Microbacterium sp002245215	91.5551	932	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339645.1	s__Microbacterium arborescens	91.3228	929	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_003610405.1	s__Microbacterium sp003610405	89.444	932	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102175.1	s__Microbacterium sp900102175	86.0783	836	1068	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876655.1	s__Microbacterium imperiale	85.7304	802	1068	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 11:53:23,738] [INFO] GTDB search result was written to GCF_028737425.1_ASM2873742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:23,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:23,744] [INFO] DFAST_QC result json was written to GCF_028737425.1_ASM2873742v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:23,744] [INFO] DFAST_QC completed!
[2024-01-24 11:53:23,744] [INFO] Total running time: 0h1m19s