[2024-01-25 17:43:50,447] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,448] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference
[2024-01-25 17:43:51,582] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,583] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,583] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf029716-1088-4853-a2a3-324081c00e05/GCF_014641475.1_ASM1464147v1_genomic.fna.gz | prodigal -d GCF_014641475.1_ASM1464147v1_genomic.fna/cds.fna -a GCF_014641475.1_ASM1464147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:58,995] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:58,996] [INFO] Task started: HMMsearch
[2024-01-25 17:43:58,996] [INFO] Running command: hmmsearch --tblout GCF_014641475.1_ASM1464147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/reference_markers.hmm GCF_014641475.1_ASM1464147v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:59,189] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:59,190] [INFO] Found 6/6 markers.
[2024-01-25 17:43:59,218] [INFO] Query marker FASTA was written to GCF_014641475.1_ASM1464147v1_genomic.fna/markers.fasta
[2024-01-25 17:43:59,218] [INFO] Task started: Blastn
[2024-01-25 17:43:59,218] [INFO] Running command: blastn -query GCF_014641475.1_ASM1464147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/reference_markers.fasta -out GCF_014641475.1_ASM1464147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:00,429] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:00,432] [INFO] Selected 12 target genomes.
[2024-01-25 17:44:00,432] [INFO] Target genome list was writen to GCF_014641475.1_ASM1464147v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:00,442] [INFO] Task started: fastANI
[2024-01-25 17:44:00,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf029716-1088-4853-a2a3-324081c00e05/GCF_014641475.1_ASM1464147v1_genomic.fna.gz --refList GCF_014641475.1_ASM1464147v1_genomic.fna/target_genomes.txt --output GCF_014641475.1_ASM1464147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:09,787] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:09,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:09,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:09,804] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:44:09,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:09,804] [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_014641475.1	1867410	1867410	type	True	100.0	1009	1009	95	conclusive
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	99.9978	1009	1009	95	conclusive
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	86.7903	798	1009	95	below_threshold
Microbacterium gubbeenense	strain=DSM 15944	GCA_000422745.1	159896	159896	type	True	82.5863	596	1009	95	below_threshold
Microbacterium indicum	strain=DSM 19969	GCA_000422385.1	358100	358100	type	True	81.7348	528	1009	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	81.0605	525	1009	95	below_threshold
Microbacterium suaedae	strain=YZYP 306	GCA_003254645.1	2067813	2067813	type	True	80.8941	521	1009	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.07	486	1009	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.3022	387	1009	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.9603	389	1009	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.3502	380	1009	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.2686	375	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:09,807] [INFO] DFAST Taxonomy check result was written to GCF_014641475.1_ASM1464147v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:09,807] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:09,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:09,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/checkm_data
[2024-01-25 17:44:09,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:09,840] [INFO] Task started: CheckM
[2024-01-25 17:44:09,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641475.1_ASM1464147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641475.1_ASM1464147v1_genomic.fna/checkm_input GCF_014641475.1_ASM1464147v1_genomic.fna/checkm_result
[2024-01-25 17:44:34,733] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:34,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:34,751] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:34,751] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:34,752] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641475.1_ASM1464147v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:34,752] [INFO] Task started: Blastn
[2024-01-25 17:44:34,752] [INFO] Running command: blastn -query GCF_014641475.1_ASM1464147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc053da3-94ef-48ca-b425-006a60319648/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641475.1_ASM1464147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:36,963] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:36,966] [INFO] Selected 8 target genomes.
[2024-01-25 17:44:36,966] [INFO] Target genome list was writen to GCF_014641475.1_ASM1464147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:36,975] [INFO] Task started: fastANI
[2024-01-25 17:44:36,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf029716-1088-4853-a2a3-324081c00e05/GCF_014641475.1_ASM1464147v1_genomic.fna.gz --refList GCF_014641475.1_ASM1464147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641475.1_ASM1464147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:42,952] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:42,959] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:42,959] [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	99.9978	1009	1009	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	86.7822	798	1009	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	82.6888	509	1009	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	82.6303	593	1009	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	81.7775	524	1009	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	81.661	601	1009	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	81.134	518	1009	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	80.9073	520	1009	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 17:44:42,960] [INFO] GTDB search result was written to GCF_014641475.1_ASM1464147v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:42,961] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:42,964] [INFO] DFAST_QC result json was written to GCF_014641475.1_ASM1464147v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:42,964] [INFO] DFAST_QC completed!
[2024-01-25 17:44:42,964] [INFO] Total running time: 0h0m53s