[2024-01-24 12:34:20,528] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,530] [INFO] DQC Reference Directory: /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference
[2024-01-24 12:34:21,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,728] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg98c5f0d0-b11c-48d8-a8da-6e2740451b61/GCF_001550065.1_ASM155006v1_genomic.fna.gz | prodigal -d GCF_001550065.1_ASM155006v1_genomic.fna/cds.fna -a GCF_001550065.1_ASM155006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:35,717] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:35,718] [INFO] Task started: HMMsearch
[2024-01-24 12:34:35,718] [INFO] Running command: hmmsearch --tblout GCF_001550065.1_ASM155006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/reference_markers.hmm GCF_001550065.1_ASM155006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:36,006] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:36,008] [INFO] Found 6/6 markers.
[2024-01-24 12:34:36,048] [INFO] Query marker FASTA was written to GCF_001550065.1_ASM155006v1_genomic.fna/markers.fasta
[2024-01-24 12:34:36,048] [INFO] Task started: Blastn
[2024-01-24 12:34:36,048] [INFO] Running command: blastn -query GCF_001550065.1_ASM155006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/reference_markers.fasta -out GCF_001550065.1_ASM155006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:36,731] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:36,734] [INFO] Selected 17 target genomes.
[2024-01-24 12:34:36,734] [INFO] Target genome list was writen to GCF_001550065.1_ASM155006v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:36,747] [INFO] Task started: fastANI
[2024-01-24 12:34:36,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c5f0d0-b11c-48d8-a8da-6e2740451b61/GCF_001550065.1_ASM155006v1_genomic.fna.gz --refList GCF_001550065.1_ASM155006v1_genomic.fna/target_genomes.txt --output GCF_001550065.1_ASM155006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:48,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:48,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:48,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:48,226] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:48,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:48,227] [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 lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	100.0	1424	1502	95	conclusive
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	84.099	941	1502	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	84.0369	934	1502	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	78.7704	418	1502	95	below_threshold
Kordiimonas gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	78.747	410	1502	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.18	401	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:48,228] [INFO] DFAST Taxonomy check result was written to GCF_001550065.1_ASM155006v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:48,229] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:48,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:48,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/checkm_data
[2024-01-24 12:34:48,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:48,276] [INFO] Task started: CheckM
[2024-01-24 12:34:48,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001550065.1_ASM155006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001550065.1_ASM155006v1_genomic.fna/checkm_input GCF_001550065.1_ASM155006v1_genomic.fna/checkm_result
[2024-01-24 12:35:31,437] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:31,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:31,461] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:31,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:31,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001550065.1_ASM155006v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:31,462] [INFO] Task started: Blastn
[2024-01-24 12:35:31,463] [INFO] Running command: blastn -query GCF_001550065.1_ASM155006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546c14aa-f060-4b22-b536-3267e38879af/dqc_reference/reference_markers_gtdb.fasta -out GCF_001550065.1_ASM155006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:32,514] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:32,518] [INFO] Selected 11 target genomes.
[2024-01-24 12:35:32,518] [INFO] Target genome list was writen to GCF_001550065.1_ASM155006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:32,527] [INFO] Task started: fastANI
[2024-01-24 12:35:32,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c5f0d0-b11c-48d8-a8da-6e2740451b61/GCF_001550065.1_ASM155006v1_genomic.fna.gz --refList GCF_001550065.1_ASM155006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001550065.1_ASM155006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:40,313] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:40,320] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:40,320] [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_001550065.1	s__Kordiimonas lipolytica	100.0	1419	1502	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_001550055.1	s__Kordiimonas lacus	84.1403	940	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCA_013372925.1	s__Kordiimonas sp013372925	79.738	492	1502	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	79.6173	480	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375545.1	s__Kordiimonas gwangyangensis	78.7807	417	1502	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	77.8134	450	1502	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	77.1762	155	1502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:35:40,322] [INFO] GTDB search result was written to GCF_001550065.1_ASM155006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:40,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:40,325] [INFO] DFAST_QC result json was written to GCF_001550065.1_ASM155006v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:40,325] [INFO] DFAST_QC completed!
[2024-01-24 12:35:40,325] [INFO] Total running time: 0h1m20s