[2024-01-25 18:12:05,588] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference
[2024-01-25 18:12:06,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,731] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cd4810f-016f-4b11-8574-7db009948b93/GCF_014656395.1_ASM1465639v1_genomic.fna.gz | prodigal -d GCF_014656395.1_ASM1465639v1_genomic.fna/cds.fna -a GCF_014656395.1_ASM1465639v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:14,743] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:14,743] [INFO] Task started: HMMsearch
[2024-01-25 18:12:14,743] [INFO] Running command: hmmsearch --tblout GCF_014656395.1_ASM1465639v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/reference_markers.hmm GCF_014656395.1_ASM1465639v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:14,963] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:14,964] [INFO] Found 6/6 markers.
[2024-01-25 18:12:14,991] [INFO] Query marker FASTA was written to GCF_014656395.1_ASM1465639v1_genomic.fna/markers.fasta
[2024-01-25 18:12:14,991] [INFO] Task started: Blastn
[2024-01-25 18:12:14,991] [INFO] Running command: blastn -query GCF_014656395.1_ASM1465639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/reference_markers.fasta -out GCF_014656395.1_ASM1465639v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:15,598] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:15,602] [INFO] Selected 23 target genomes.
[2024-01-25 18:12:15,602] [INFO] Target genome list was writen to GCF_014656395.1_ASM1465639v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:15,640] [INFO] Task started: fastANI
[2024-01-25 18:12:15,640] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd4810f-016f-4b11-8574-7db009948b93/GCF_014656395.1_ASM1465639v1_genomic.fna.gz --refList GCF_014656395.1_ASM1465639v1_genomic.fna/target_genomes.txt --output GCF_014656395.1_ASM1465639v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:30,733] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:30,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:30,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:30,739] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:30,739] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:30,739] [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
Kordiimonas sediminis	strain=KCTC 42590	GCA_014656395.1	1735581	1735581	type	True	100.0	1076	1076	95	conclusive
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	77.1688	77	1076	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	77.1233	94	1076	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	77.0644	95	1076	95	below_threshold
Kordiimonas laminariae	strain=5E331	GCA_023008165.1	2917717	2917717	type	True	77.0217	74	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,741] [INFO] DFAST Taxonomy check result was written to GCF_014656395.1_ASM1465639v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:30,742] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:30,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:30,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/checkm_data
[2024-01-25 18:12:30,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:30,780] [INFO] Task started: CheckM
[2024-01-25 18:12:30,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656395.1_ASM1465639v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656395.1_ASM1465639v1_genomic.fna/checkm_input GCF_014656395.1_ASM1465639v1_genomic.fna/checkm_result
[2024-01-25 18:12:58,053] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:58,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:58,071] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:58,071] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:58,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656395.1_ASM1465639v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:58,072] [INFO] Task started: Blastn
[2024-01-25 18:12:58,072] [INFO] Running command: blastn -query GCF_014656395.1_ASM1465639v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbac3108f-4d6d-4681-afa2-6d434101009d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656395.1_ASM1465639v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:59,153] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:59,156] [INFO] Selected 21 target genomes.
[2024-01-25 18:12:59,156] [INFO] Target genome list was writen to GCF_014656395.1_ASM1465639v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:59,190] [INFO] Task started: fastANI
[2024-01-25 18:12:59,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd4810f-016f-4b11-8574-7db009948b93/GCF_014656395.1_ASM1465639v1_genomic.fna.gz --refList GCF_014656395.1_ASM1465639v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656395.1_ASM1465639v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:11,748] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:11,753] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:11,753] [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_014656395.1	s__Kordiimonas sediminis	100.0	1076	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001550065.1	s__Kordiimonas lipolytica	77.2006	77	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550055.1	s__Kordiimonas lacus	77.1488	93	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCA_017640725.1	s__Kordiimonas sp017640725	76.9031	59	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCF_000375545.1	s__Kordiimonas gwangyangensis	76.351	72	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCA_006226495.1	s__Kordiimonas sp006226495	76.283	56	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:11,755] [INFO] GTDB search result was written to GCF_014656395.1_ASM1465639v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:11,755] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:11,757] [INFO] DFAST_QC result json was written to GCF_014656395.1_ASM1465639v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:11,758] [INFO] DFAST_QC completed!
[2024-01-25 18:13:11,758] [INFO] Total running time: 0h1m6s