[2024-01-25 20:20:35,773] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:35,775] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:35,775] [INFO] DQC Reference Directory: /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference
[2024-01-25 20:20:36,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:36,910] [INFO] Task started: Prodigal
[2024-01-25 20:20:36,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg5682a971-0ae4-45db-ae15-61768f989bac/GCF_027921865.1_ASM2792186v1_genomic.fna.gz | prodigal -d GCF_027921865.1_ASM2792186v1_genomic.fna/cds.fna -a GCF_027921865.1_ASM2792186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:44,536] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:44,536] [INFO] Task started: HMMsearch
[2024-01-25 20:20:44,536] [INFO] Running command: hmmsearch --tblout GCF_027921865.1_ASM2792186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/reference_markers.hmm GCF_027921865.1_ASM2792186v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:44,785] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:44,786] [INFO] Found 6/6 markers.
[2024-01-25 20:20:44,822] [INFO] Query marker FASTA was written to GCF_027921865.1_ASM2792186v1_genomic.fna/markers.fasta
[2024-01-25 20:20:44,823] [INFO] Task started: Blastn
[2024-01-25 20:20:44,823] [INFO] Running command: blastn -query GCF_027921865.1_ASM2792186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/reference_markers.fasta -out GCF_027921865.1_ASM2792186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:45,986] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:45,989] [INFO] Selected 22 target genomes.
[2024-01-25 20:20:45,989] [INFO] Target genome list was writen to GCF_027921865.1_ASM2792186v1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:46,017] [INFO] Task started: fastANI
[2024-01-25 20:20:46,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg5682a971-0ae4-45db-ae15-61768f989bac/GCF_027921865.1_ASM2792186v1_genomic.fna.gz --refList GCF_027921865.1_ASM2792186v1_genomic.fna/target_genomes.txt --output GCF_027921865.1_ASM2792186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:01,544] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:01,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:01,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:01,557] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:01,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:01,558] [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	99.9602	1004	1018	95	conclusive
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	84.2388	735	1018	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	81.6053	542	1018	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.5185	592	1018	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	81.4548	535	1018	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	81.3221	549	1018	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	81.2923	550	1018	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	81.276	562	1018	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.1374	529	1018	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	81.1207	527	1018	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.0063	508	1018	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	80.9714	509	1018	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.91	548	1018	95	below_threshold
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	80.8077	546	1018	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	80.743	554	1018	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	80.735	537	1018	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	80.7278	538	1018	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.5836	505	1018	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.5265	541	1018	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	80.3889	521	1018	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.3376	531	1018	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	79.3857	394	1018	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:01,559] [INFO] DFAST Taxonomy check result was written to GCF_027921865.1_ASM2792186v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:01,560] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:01,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:01,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/checkm_data
[2024-01-25 20:21:01,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:01,594] [INFO] Task started: CheckM
[2024-01-25 20:21:01,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921865.1_ASM2792186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921865.1_ASM2792186v1_genomic.fna/checkm_input GCF_027921865.1_ASM2792186v1_genomic.fna/checkm_result
[2024-01-25 20:21:42,129] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:42,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:42,147] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:42,147] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:42,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921865.1_ASM2792186v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:42,148] [INFO] Task started: Blastn
[2024-01-25 20:21:42,148] [INFO] Running command: blastn -query GCF_027921865.1_ASM2792186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfee956ea-1c06-4b6d-91c0-00cacb50e5f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921865.1_ASM2792186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:43,972] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:43,975] [INFO] Selected 8 target genomes.
[2024-01-25 20:21:43,975] [INFO] Target genome list was writen to GCF_027921865.1_ASM2792186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:43,983] [INFO] Task started: fastANI
[2024-01-25 20:21:43,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg5682a971-0ae4-45db-ae15-61768f989bac/GCF_027921865.1_ASM2792186v1_genomic.fna.gz --refList GCF_027921865.1_ASM2792186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921865.1_ASM2792186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:50,490] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:50,496] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:50,496] [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_017876655.1	s__Microbacterium imperiale	99.9602	1004	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002245215.1	s__Microbacterium sp002245215	85.7644	833	1018	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	85.7096	795	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_003289625.1	s__Microbacterium sp003289625	85.5148	805	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.69	98.69	0.93	0.93	2	-
GCF_013389665.1	s__Microbacterium oleivorans_C	85.1691	760	1018	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	85.1344	785	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610405.1	s__Microbacterium sp003610405	85.0734	812	1018	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	81.4606	597	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:50,497] [INFO] GTDB search result was written to GCF_027921865.1_ASM2792186v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:50,499] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:50,502] [INFO] DFAST_QC result json was written to GCF_027921865.1_ASM2792186v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:50,502] [INFO] DFAST_QC completed!
[2024-01-25 20:21:50,502] [INFO] Total running time: 0h1m15s