[2024-01-24 14:07:14,544] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference
[2024-01-24 14:07:15,876] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:15,877] [INFO] Task started: Prodigal
[2024-01-24 14:07:15,878] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d51e4bb-c3cd-43f4-be69-7fbadd0fa546/GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/cds.fna -a GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:26,173] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:26,173] [INFO] Task started: HMMsearch
[2024-01-24 14:07:26,173] [INFO] Running command: hmmsearch --tblout GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/reference_markers.hmm GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:26,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:26,438] [INFO] Found 6/6 markers.
[2024-01-24 14:07:26,470] [INFO] Query marker FASTA was written to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:07:26,470] [INFO] Task started: Blastn
[2024-01-24 14:07:26,470] [INFO] Running command: blastn -query GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/reference_markers.fasta -out GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:27,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:27,626] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:27,627] [INFO] Target genome list was writen to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:07:27,650] [INFO] Task started: fastANI
[2024-01-24 14:07:27,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d51e4bb-c3cd-43f4-be69-7fbadd0fa546/GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna.gz --refList GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:38,762] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:38,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:38,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:38,777] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:38,778] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:38,778] [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 paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	100.0	1175	1184	95	conclusive
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	99.801	1004	1184	95	conclusive
Microbacterium algeriense	strain=G1	GCA_008868005.1	2615184	2615184	type	True	85.1082	909	1184	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	83.9023	856	1184	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	83.8957	864	1184	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	83.7919	747	1184	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	83.686	757	1184	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	82.8645	762	1184	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	82.8228	732	1184	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	81.6133	572	1184	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	81.4273	587	1184	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.0387	481	1184	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.0346	462	1184	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	79.926	466	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,780] [INFO] DFAST Taxonomy check result was written to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:07:38,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:38,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:38,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/checkm_data
[2024-01-24 14:07:38,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:38,817] [INFO] Task started: CheckM
[2024-01-24 14:07:38,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/checkm_input GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:08:37,735] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:37,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:37,751] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:37,752] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:37,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:08:37,752] [INFO] Task started: Blastn
[2024-01-24 14:08:37,753] [INFO] Running command: blastn -query GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e4f4327-5cb8-4ab3-93fd-3d6f0200c8f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:39,730] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:39,739] [INFO] Selected 7 target genomes.
[2024-01-24 14:08:39,740] [INFO] Target genome list was writen to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:39,746] [INFO] Task started: fastANI
[2024-01-24 14:08:39,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d51e4bb-c3cd-43f4-be69-7fbadd0fa546/GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna.gz --refList GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:46,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:46,977] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:46,977] [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_900105335.1	s__Microbacterium paraoxydans	100.0	1180	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	conclusive
GCF_019056515.1	s__Microbacterium sp001595495	95.3562	1030	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	98.29	96.93	0.91	0.85	10	-
GCF_001866135.1	s__Microbacterium sp001866135	95.261	997	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.261	97.41	95.65	0.93	0.91	3	conclusive
GCF_904066215.1	s__Microbacterium sp002456035	93.3183	1034	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.68	98.64	0.94	0.94	3	-
GCF_002848265.1	s__Microbacterium sp002848265	92.3105	1007	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939615.1	s__Microbacterium sp017939615	90.1063	939	1184	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271365.1	s__Microbacterium sp008271365	90.0228	1013	1184	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 14:08:46,979] [INFO] GTDB search result was written to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:46,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:46,983] [INFO] DFAST_QC result json was written to GCF_900105335.1_IMG-taxon_2634166897_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:46,983] [INFO] DFAST_QC completed!
[2024-01-24 14:08:46,983] [INFO] Total running time: 0h1m32s