[2024-01-24 13:19:10,384] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:10,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:10,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference
[2024-01-24 13:19:11,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:11,681] [INFO] Task started: Prodigal
[2024-01-24 13:19:11,681] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1a702da-6261-4763-8a2d-645432ca6b0a/GCF_000616065.1_ASM61606v1_genomic.fna.gz | prodigal -d GCF_000616065.1_ASM61606v1_genomic.fna/cds.fna -a GCF_000616065.1_ASM61606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:25,328] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:25,329] [INFO] Task started: HMMsearch
[2024-01-24 13:19:25,329] [INFO] Running command: hmmsearch --tblout GCF_000616065.1_ASM61606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/reference_markers.hmm GCF_000616065.1_ASM61606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:25,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:25,587] [INFO] Found 6/6 markers.
[2024-01-24 13:19:25,633] [INFO] Query marker FASTA was written to GCF_000616065.1_ASM61606v1_genomic.fna/markers.fasta
[2024-01-24 13:19:25,633] [INFO] Task started: Blastn
[2024-01-24 13:19:25,633] [INFO] Running command: blastn -query GCF_000616065.1_ASM61606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/reference_markers.fasta -out GCF_000616065.1_ASM61606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,429] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:26,429] [INFO] Target genome list was writen to GCF_000616065.1_ASM61606v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:26,441] [INFO] Task started: fastANI
[2024-01-24 13:19:26,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a702da-6261-4763-8a2d-645432ca6b0a/GCF_000616065.1_ASM61606v1_genomic.fna.gz --refList GCF_000616065.1_ASM61606v1_genomic.fna/target_genomes.txt --output GCF_000616065.1_ASM61606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:38,617] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:38,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:38,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:38,631] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:38,631] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:38,632] [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 gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	100.0	1336	1336	95	conclusive
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	99.9603	1334	1336	95	conclusive
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	78.7317	412	1336	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.5101	429	1336	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	78.4566	436	1336	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.3869	379	1336	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.4149	81	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:38,633] [INFO] DFAST Taxonomy check result was written to GCF_000616065.1_ASM61606v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:38,634] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:38,634] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:38,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/checkm_data
[2024-01-24 13:19:38,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:38,679] [INFO] Task started: CheckM
[2024-01-24 13:19:38,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000616065.1_ASM61606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000616065.1_ASM61606v1_genomic.fna/checkm_input GCF_000616065.1_ASM61606v1_genomic.fna/checkm_result
[2024-01-24 13:20:19,265] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:19,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:19,430] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:19,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:19,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000616065.1_ASM61606v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:19,432] [INFO] Task started: Blastn
[2024-01-24 13:20:19,432] [INFO] Running command: blastn -query GCF_000616065.1_ASM61606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0de88db4-819e-4a8b-a5e6-61714f5657d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000616065.1_ASM61606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:20,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:20,734] [INFO] Selected 18 target genomes.
[2024-01-24 13:20:20,734] [INFO] Target genome list was writen to GCF_000616065.1_ASM61606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:20,770] [INFO] Task started: fastANI
[2024-01-24 13:20:20,771] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1a702da-6261-4763-8a2d-645432ca6b0a/GCF_000616065.1_ASM61606v1_genomic.fna.gz --refList GCF_000616065.1_ASM61606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000616065.1_ASM61606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:32,918] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:32,931] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:32,931] [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_000375545.1	s__Kordiimonas gwangyangensis	99.9603	1334	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	conclusive
GCF_001550065.1	s__Kordiimonas lipolytica	78.7323	412	1336	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	78.4633	429	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCA_006226495.1	s__Kordiimonas sp006226495	78.115	443	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372975.1	s__Kordiimonas sp013372975	77.6362	260	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	77.3439	255	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640725.1	s__Kordiimonas sp017640725	76.684	122	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCA_016764715.1	s__Kordiimonas sp016764715	76.1585	67	1336	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:32,933] [INFO] GTDB search result was written to GCF_000616065.1_ASM61606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:32,933] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:32,936] [INFO] DFAST_QC result json was written to GCF_000616065.1_ASM61606v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:32,936] [INFO] DFAST_QC completed!
[2024-01-24 13:20:32,937] [INFO] Total running time: 0h1m23s