[2024-01-24 15:10:39,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:39,889] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:39,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference
[2024-01-24 15:10:41,155] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:41,156] [INFO] Task started: Prodigal
[2024-01-24 15:10:41,156] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb1998c6-910e-440d-8950-84c27c6a8322/GCF_006783905.1_ASM678390v1_genomic.fna.gz | prodigal -d GCF_006783905.1_ASM678390v1_genomic.fna/cds.fna -a GCF_006783905.1_ASM678390v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:54,283] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:54,284] [INFO] Task started: HMMsearch
[2024-01-24 15:10:54,284] [INFO] Running command: hmmsearch --tblout GCF_006783905.1_ASM678390v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/reference_markers.hmm GCF_006783905.1_ASM678390v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:54,590] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:54,592] [INFO] Found 6/6 markers.
[2024-01-24 15:10:54,633] [INFO] Query marker FASTA was written to GCF_006783905.1_ASM678390v1_genomic.fna/markers.fasta
[2024-01-24 15:10:54,633] [INFO] Task started: Blastn
[2024-01-24 15:10:54,633] [INFO] Running command: blastn -query GCF_006783905.1_ASM678390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/reference_markers.fasta -out GCF_006783905.1_ASM678390v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:55,955] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:55,958] [INFO] Selected 12 target genomes.
[2024-01-24 15:10:55,958] [INFO] Target genome list was writen to GCF_006783905.1_ASM678390v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:55,962] [INFO] Task started: fastANI
[2024-01-24 15:10:55,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1998c6-910e-440d-8950-84c27c6a8322/GCF_006783905.1_ASM678390v1_genomic.fna.gz --refList GCF_006783905.1_ASM678390v1_genomic.fna/target_genomes.txt --output GCF_006783905.1_ASM678390v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:07,944] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:07,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:07,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:07,955] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:07,955] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:07,955] [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 kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	100.0	1412	1422	95	conclusive
Microbacterium helvum	strain=NEAU-LLC	GCA_014779795.1	2773713	2773713	type	True	87.6392	1052	1422	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	84.4043	891	1422	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	84.3843	957	1422	95	below_threshold
Microbacterium ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	84.2804	931	1422	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	84.0891	963	1422	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	83.4788	840	1422	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	83.4116	778	1422	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	82.8112	726	1422	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	82.3889	761	1422	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	81.365	625	1422	95	below_threshold
Microbacterium protaetiae	strain=DFW100M-13	GCA_004135285.1	2509458	2509458	type	True	79.7812	532	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:07,957] [INFO] DFAST Taxonomy check result was written to GCF_006783905.1_ASM678390v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:07,957] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:07,957] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:07,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/checkm_data
[2024-01-24 15:11:07,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:08,000] [INFO] Task started: CheckM
[2024-01-24 15:11:08,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006783905.1_ASM678390v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006783905.1_ASM678390v1_genomic.fna/checkm_input GCF_006783905.1_ASM678390v1_genomic.fna/checkm_result
[2024-01-24 15:12:16,254] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:16,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:16,277] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:16,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:16,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006783905.1_ASM678390v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:16,279] [INFO] Task started: Blastn
[2024-01-24 15:12:16,279] [INFO] Running command: blastn -query GCF_006783905.1_ASM678390v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42374ecb-81ec-4575-b541-a6ae57b02475/dqc_reference/reference_markers_gtdb.fasta -out GCF_006783905.1_ASM678390v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:18,278] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:18,281] [INFO] Selected 13 target genomes.
[2024-01-24 15:12:18,282] [INFO] Target genome list was writen to GCF_006783905.1_ASM678390v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:18,291] [INFO] Task started: fastANI
[2024-01-24 15:12:18,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1998c6-910e-440d-8950-84c27c6a8322/GCF_006783905.1_ASM678390v1_genomic.fna.gz --refList GCF_006783905.1_ASM678390v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006783905.1_ASM678390v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:31,611] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:31,622] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:31,623] [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_006783905.1	s__Microbacterium kyungheense	100.0	1414	1422	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_000380605.1	s__Microbacterium sp000380605	87.9696	1051	1422	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	87.6518	1051	1422	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	84.5681	946	1422	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	84.3714	894	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956465.1	s__Microbacterium trichothecenolyticum	84.3708	958	1422	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	84.2635	933	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_009858275.1	s__Microbacterium sp009858275	84.1363	866	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	84.0761	821	1422	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	83.9369	900	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.26	99.26	0.95	0.95	2	-
GCA_001898315.1	s__Microbacterium sp001898315	81.3198	587	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001314225.1	s__Microbacterium sp001314225	80.7008	604	1422	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135285.1	s__Microbacterium protaetiae	79.7776	529	1422	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 15:12:31,624] [INFO] GTDB search result was written to GCF_006783905.1_ASM678390v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:31,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:31,628] [INFO] DFAST_QC result json was written to GCF_006783905.1_ASM678390v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:31,629] [INFO] DFAST_QC completed!
[2024-01-24 15:12:31,629] [INFO] Total running time: 0h1m52s