[2024-01-25 18:09:50,743] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:09:50,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:09:50,745] [INFO] DQC Reference Directory: /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference
[2024-01-25 18:09:51,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:09:51,934] [INFO] Task started: Prodigal
[2024-01-25 18:09:51,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c055dff-3156-4839-a5f0-0cf3ab210564/GCF_003327285.1_ASM332728v1_genomic.fna.gz | prodigal -d GCF_003327285.1_ASM332728v1_genomic.fna/cds.fna -a GCF_003327285.1_ASM332728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:09:59,488] [INFO] Task succeeded: Prodigal
[2024-01-25 18:09:59,488] [INFO] Task started: HMMsearch
[2024-01-25 18:09:59,488] [INFO] Running command: hmmsearch --tblout GCF_003327285.1_ASM332728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/reference_markers.hmm GCF_003327285.1_ASM332728v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:09:59,770] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:09:59,771] [INFO] Found 6/6 markers.
[2024-01-25 18:09:59,796] [INFO] Query marker FASTA was written to GCF_003327285.1_ASM332728v1_genomic.fna/markers.fasta
[2024-01-25 18:09:59,797] [INFO] Task started: Blastn
[2024-01-25 18:09:59,797] [INFO] Running command: blastn -query GCF_003327285.1_ASM332728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/reference_markers.fasta -out GCF_003327285.1_ASM332728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:01,092] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:01,096] [INFO] Selected 12 target genomes.
[2024-01-25 18:10:01,096] [INFO] Target genome list was writen to GCF_003327285.1_ASM332728v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:01,119] [INFO] Task started: fastANI
[2024-01-25 18:10:01,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c055dff-3156-4839-a5f0-0cf3ab210564/GCF_003327285.1_ASM332728v1_genomic.fna.gz --refList GCF_003327285.1_ASM332728v1_genomic.fna/target_genomes.txt --output GCF_003327285.1_ASM332728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:10,199] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:10,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:10,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:10,209] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:10:10,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:10,209] [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 sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	100.0	1011	1012	95	conclusive
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	99.9956	1007	1012	95	conclusive
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	86.7249	803	1012	95	below_threshold
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	82.6973	585	1012	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	81.7486	536	1012	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	81.2398	521	1012	95	below_threshold
Microbacterium suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	80.8942	511	1012	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.2524	466	1012	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.3985	375	1012	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.9368	388	1012	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.2796	388	1012	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.1276	392	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:10,211] [INFO] DFAST Taxonomy check result was written to GCF_003327285.1_ASM332728v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:10,211] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:10,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:10,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/checkm_data
[2024-01-25 18:10:10,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:10,245] [INFO] Task started: CheckM
[2024-01-25 18:10:10,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003327285.1_ASM332728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003327285.1_ASM332728v1_genomic.fna/checkm_input GCF_003327285.1_ASM332728v1_genomic.fna/checkm_result
[2024-01-25 18:10:35,895] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:35,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:35,924] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:35,924] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:35,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003327285.1_ASM332728v1_genomic.fna/markers.fasta)
[2024-01-25 18:10:35,925] [INFO] Task started: Blastn
[2024-01-25 18:10:35,926] [INFO] Running command: blastn -query GCF_003327285.1_ASM332728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc15bd30c-672e-4fc2-803e-df70d2af84bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003327285.1_ASM332728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:38,117] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:38,120] [INFO] Selected 8 target genomes.
[2024-01-25 18:10:38,120] [INFO] Target genome list was writen to GCF_003327285.1_ASM332728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:38,134] [INFO] Task started: fastANI
[2024-01-25 18:10:38,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c055dff-3156-4839-a5f0-0cf3ab210564/GCF_003327285.1_ASM332728v1_genomic.fna.gz --refList GCF_003327285.1_ASM332728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003327285.1_ASM332728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:43,924] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:43,930] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:43,930] [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_003327285.1	s__Microbacterium sorbitolivorans	100.0	1011	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014646015.1	s__Microbacterium nanhaiense	86.6945	805	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422745.1	s__Microbacterium gubbeenense	82.73	583	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117025.1	s__Microbacterium stercoravium	82.5988	521	1012	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	81.7612	535	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009745985.1	s__Microbacterium karelineae	81.6394	601	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326725.1	s__Microbacterium excoecariae	81.2292	520	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_003254645.1	s__Microbacterium suaedae	80.9413	507	1012	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:43,931] [INFO] GTDB search result was written to GCF_003327285.1_ASM332728v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:43,932] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:43,934] [INFO] DFAST_QC result json was written to GCF_003327285.1_ASM332728v1_genomic.fna/dqc_result.json
[2024-01-25 18:10:43,934] [INFO] DFAST_QC completed!
[2024-01-25 18:10:43,934] [INFO] Total running time: 0h0m53s