[2024-01-24 13:17:13,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:13,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:13,832] [INFO] DQC Reference Directory: /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference
[2024-01-24 13:17:15,162] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:15,163] [INFO] Task started: Prodigal
[2024-01-24 13:17:15,163] [INFO] Running command: gunzip -c /var/lib/cwl/stg245d6bec-a3ec-4fae-b085-75cc37ae7313/GCF_000422745.1_ASM42274v1_genomic.fna.gz | prodigal -d GCF_000422745.1_ASM42274v1_genomic.fna/cds.fna -a GCF_000422745.1_ASM42274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:23,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:23,463] [INFO] Task started: HMMsearch
[2024-01-24 13:17:23,463] [INFO] Running command: hmmsearch --tblout GCF_000422745.1_ASM42274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/reference_markers.hmm GCF_000422745.1_ASM42274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:23,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:23,723] [INFO] Found 6/6 markers.
[2024-01-24 13:17:23,754] [INFO] Query marker FASTA was written to GCF_000422745.1_ASM42274v1_genomic.fna/markers.fasta
[2024-01-24 13:17:23,754] [INFO] Task started: Blastn
[2024-01-24 13:17:23,754] [INFO] Running command: blastn -query GCF_000422745.1_ASM42274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/reference_markers.fasta -out GCF_000422745.1_ASM42274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:24,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:24,991] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:24,991] [INFO] Target genome list was writen to GCF_000422745.1_ASM42274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:24,998] [INFO] Task started: fastANI
[2024-01-24 13:17:24,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg245d6bec-a3ec-4fae-b085-75cc37ae7313/GCF_000422745.1_ASM42274v1_genomic.fna.gz --refList GCF_000422745.1_ASM42274v1_genomic.fna/target_genomes.txt --output GCF_000422745.1_ASM42274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:36,027] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:36,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:36,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:36,049] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:36,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:36,050] [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 gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	100.0	966	968	95	conclusive
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	82.5802	602	968	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	82.4751	599	968	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	82.0602	573	968	95	below_threshold
Microbacterium faecale	strain=CGMCC 1.15152	GCA_014640975.1	1804630	1804630	type	True	81.5203	535	968	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	81.5093	493	968	95	below_threshold
Microbacterium suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	81.3653	530	968	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	81.2564	512	968	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	80.7539	493	968	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	79.8943	439	968	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.196	345	968	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.1191	364	968	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	78.8261	342	968	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.7975	373	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:36,051] [INFO] DFAST Taxonomy check result was written to GCF_000422745.1_ASM42274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:36,052] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:36,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:36,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/checkm_data
[2024-01-24 13:17:36,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:36,085] [INFO] Task started: CheckM
[2024-01-24 13:17:36,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000422745.1_ASM42274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000422745.1_ASM42274v1_genomic.fna/checkm_input GCF_000422745.1_ASM42274v1_genomic.fna/checkm_result
[2024-01-24 13:18:05,885] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:05,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:05,908] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:05,908] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:05,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000422745.1_ASM42274v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:05,909] [INFO] Task started: Blastn
[2024-01-24 13:18:05,910] [INFO] Running command: blastn -query GCF_000422745.1_ASM42274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbafbfdaa-373d-4dcc-bb67-c55ec38368e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000422745.1_ASM42274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,022] [INFO] Selected 9 target genomes.
[2024-01-24 13:18:08,022] [INFO] Target genome list was writen to GCF_000422745.1_ASM42274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:08,029] [INFO] Task started: fastANI
[2024-01-24 13:18:08,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg245d6bec-a3ec-4fae-b085-75cc37ae7313/GCF_000422745.1_ASM42274v1_genomic.fna.gz --refList GCF_000422745.1_ASM42274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000422745.1_ASM42274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:14,976] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:14,984] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:14,985] [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_000422745.1	s__Microbacterium gubbeenense	100.0	966	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019117025.1	s__Microbacterium stercoravium	87.0667	594	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	82.5667	602	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009745985.1	s__Microbacterium karelineae	82.056	596	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646015.1	s__Microbacterium nanhaiense	82.0422	574	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422385.1	s__Microbacterium indicum	81.5556	489	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640975.1	s__Microbacterium faecale	81.5201	535	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.13	95.13	0.92	0.92	2	-
GCF_003254645.1	s__Microbacterium suaedae	81.3349	533	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	81.2485	514	968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:14,987] [INFO] GTDB search result was written to GCF_000422745.1_ASM42274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:14,987] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:14,991] [INFO] DFAST_QC result json was written to GCF_000422745.1_ASM42274v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:14,991] [INFO] DFAST_QC completed!
[2024-01-24 13:18:14,991] [INFO] Total running time: 0h1m1s