[2024-01-24 12:13:57,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:57,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:57,679] [INFO] DQC Reference Directory: /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference
[2024-01-24 12:13:59,069] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:59,072] [INFO] Task started: Prodigal
[2024-01-24 12:13:59,072] [INFO] Running command: gunzip -c /var/lib/cwl/stg4767fdeb-c460-445b-a5f4-17d133a47f0f/GCF_000375545.1_ASM37554v1_genomic.fna.gz | prodigal -d GCF_000375545.1_ASM37554v1_genomic.fna/cds.fna -a GCF_000375545.1_ASM37554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:13,343] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:13,344] [INFO] Task started: HMMsearch
[2024-01-24 12:14:13,344] [INFO] Running command: hmmsearch --tblout GCF_000375545.1_ASM37554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/reference_markers.hmm GCF_000375545.1_ASM37554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:13,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:13,650] [INFO] Found 6/6 markers.
[2024-01-24 12:14:13,690] [INFO] Query marker FASTA was written to GCF_000375545.1_ASM37554v1_genomic.fna/markers.fasta
[2024-01-24 12:14:13,690] [INFO] Task started: Blastn
[2024-01-24 12:14:13,690] [INFO] Running command: blastn -query GCF_000375545.1_ASM37554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/reference_markers.fasta -out GCF_000375545.1_ASM37554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:14,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:14,485] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:14,485] [INFO] Target genome list was writen to GCF_000375545.1_ASM37554v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:14,510] [INFO] Task started: fastANI
[2024-01-24 12:14:14,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg4767fdeb-c460-445b-a5f4-17d133a47f0f/GCF_000375545.1_ASM37554v1_genomic.fna.gz --refList GCF_000375545.1_ASM37554v1_genomic.fna/target_genomes.txt --output GCF_000375545.1_ASM37554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:25,680] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:25,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:25,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:25,688] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:25,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:25,688] [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=DSM 19435	GCA_000375545.1	288022	288022	type	True	100.0	1354	1354	95	conclusive
Kordiimonas gwangyangensis	strain=JCM 12864	GCA_000616065.1	288022	288022	type	True	99.944	1326	1354	95	conclusive
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	78.6974	401	1354	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	78.5311	429	1354	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.5197	436	1354	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.4327	382	1354	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.0409	86	1354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:25,690] [INFO] DFAST Taxonomy check result was written to GCF_000375545.1_ASM37554v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:25,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:25,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:25,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/checkm_data
[2024-01-24 12:14:25,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:25,737] [INFO] Task started: CheckM
[2024-01-24 12:14:25,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000375545.1_ASM37554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000375545.1_ASM37554v1_genomic.fna/checkm_input GCF_000375545.1_ASM37554v1_genomic.fna/checkm_result
[2024-01-24 12:15:10,478] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:10,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:10,500] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:10,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:10,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000375545.1_ASM37554v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:10,501] [INFO] Task started: Blastn
[2024-01-24 12:15:10,501] [INFO] Running command: blastn -query GCF_000375545.1_ASM37554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga593a937-3841-44e8-9126-31190fb3e08a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000375545.1_ASM37554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:11,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:11,780] [INFO] Selected 16 target genomes.
[2024-01-24 12:15:11,781] [INFO] Target genome list was writen to GCF_000375545.1_ASM37554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:11,812] [INFO] Task started: fastANI
[2024-01-24 12:15:11,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg4767fdeb-c460-445b-a5f4-17d133a47f0f/GCF_000375545.1_ASM37554v1_genomic.fna.gz --refList GCF_000375545.1_ASM37554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000375545.1_ASM37554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:23,146] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:23,161] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:23,162] [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	100.0	1354	1354	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	78.7084	401	1354	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	78.5197	436	1354	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	78.1415	451	1354	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	77.6804	256	1354	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	77.5243	250	1354	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	76.9257	122	1354	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	76.0076	61	1354	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 12:15:23,165] [INFO] GTDB search result was written to GCF_000375545.1_ASM37554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:23,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:23,173] [INFO] DFAST_QC result json was written to GCF_000375545.1_ASM37554v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:23,173] [INFO] DFAST_QC completed!
[2024-01-24 12:15:23,173] [INFO] Total running time: 0h1m25s