[2024-01-24 14:06:05,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:05,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:05,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference
[2024-01-24 14:06:07,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,134] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,134] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e7d4325-67b3-4a55-949a-8bd188b35545/GCF_006716815.1_ASM671681v1_genomic.fna.gz | prodigal -d GCF_006716815.1_ASM671681v1_genomic.fna/cds.fna -a GCF_006716815.1_ASM671681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,297] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,298] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,298] [INFO] Running command: hmmsearch --tblout GCF_006716815.1_ASM671681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/reference_markers.hmm GCF_006716815.1_ASM671681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:16,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:16,543] [INFO] Found 6/6 markers.
[2024-01-24 14:06:16,577] [INFO] Query marker FASTA was written to GCF_006716815.1_ASM671681v1_genomic.fna/markers.fasta
[2024-01-24 14:06:16,577] [INFO] Task started: Blastn
[2024-01-24 14:06:16,577] [INFO] Running command: blastn -query GCF_006716815.1_ASM671681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/reference_markers.fasta -out GCF_006716815.1_ASM671681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,918] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,921] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:17,922] [INFO] Target genome list was writen to GCF_006716815.1_ASM671681v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,931] [INFO] Task started: fastANI
[2024-01-24 14:06:17,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e7d4325-67b3-4a55-949a-8bd188b35545/GCF_006716815.1_ASM671681v1_genomic.fna.gz --refList GCF_006716815.1_ASM671681v1_genomic.fna/target_genomes.txt --output GCF_006716815.1_ASM671681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:28,527] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:28,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:28,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:28,541] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:28,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:28,541] [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 lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	100.0	1021	1026	95	conclusive
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	99.8843	877	1026	95	conclusive
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	99.8807	872	1026	95	conclusive
Microbacterium paulum	strain=2C	GCA_015707995.1	2707006	2707006	type	True	88.4561	704	1026	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	84.4092	670	1026	95	below_threshold
Microbacterium dextranolyticum	strain=DSM 8607	GCA_016907295.1	36806	36806	type	True	83.8895	630	1026	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	83.3386	610	1026	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	82.7106	615	1026	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	81.3851	534	1026	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	81.3059	537	1026	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	81.2339	543	1026	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.7538	543	1026	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:28,544] [INFO] DFAST Taxonomy check result was written to GCF_006716815.1_ASM671681v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:28,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:28,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:28,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/checkm_data
[2024-01-24 14:06:28,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:28,580] [INFO] Task started: CheckM
[2024-01-24 14:06:28,580] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716815.1_ASM671681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716815.1_ASM671681v1_genomic.fna/checkm_input GCF_006716815.1_ASM671681v1_genomic.fna/checkm_result
[2024-01-24 14:07:13,581] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:13,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,599] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:13,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:13,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716815.1_ASM671681v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:13,601] [INFO] Task started: Blastn
[2024-01-24 14:07:13,601] [INFO] Running command: blastn -query GCF_006716815.1_ASM671681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0055b6c6-405c-4849-a122-36d495c3199c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716815.1_ASM671681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:15,693] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:15,697] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:15,697] [INFO] Target genome list was writen to GCF_006716815.1_ASM671681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:15,720] [INFO] Task started: fastANI
[2024-01-24 14:07:15,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e7d4325-67b3-4a55-949a-8bd188b35545/GCF_006716815.1_ASM671681v1_genomic.fna.gz --refList GCF_006716815.1_ASM671681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716815.1_ASM671681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:26,791] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:26,814] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:26,814] [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_006716815.1	s__Microbacterium lacticum	100.0	1022	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	97.16	0.92	0.78	4	conclusive
GCF_015707995.1	s__Microbacterium sp015707995	88.4827	702	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907815.1	s__Microbacterium aurum	84.4079	666	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.09	96.17	0.91	0.83	3	-
GCA_017305435.1	s__Microbacterium sp017305435	84.2837	669	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248655.1	s__Microbacterium sp003248655	84.0904	607	1026	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	84.0772	641	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_016907295.1	s__Microbacterium dextranolyticum	83.8691	631	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724425.1	s__Microbacterium sp001724425	83.5734	587	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_018717645.1	s__Microbacterium flavum	83.4736	678	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592125.1	s__Microbacterium hominis	83.2974	615	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.96	98.42	0.92	0.89	6	-
GCF_016807485.1	s__Microbacterium sp016807485	82.8254	396	1026	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	82.6707	618	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907555.1	s__Microbacterium laevaniformans	82.6441	627	1026	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.33	96.04	0.85	0.81	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,817] [INFO] GTDB search result was written to GCF_006716815.1_ASM671681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:26,817] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:26,821] [INFO] DFAST_QC result json was written to GCF_006716815.1_ASM671681v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:26,822] [INFO] DFAST_QC completed!
[2024-01-24 14:07:26,822] [INFO] Total running time: 0h1m21s