[2024-01-24 13:12:56,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:56,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:56,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference
[2024-01-24 13:12:57,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,466] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg91be0d62-78f6-4d44-bba0-271b73d2d22c/GCF_009797935.1_ASM979793v1_genomic.fna.gz | prodigal -d GCF_009797935.1_ASM979793v1_genomic.fna/cds.fna -a GCF_009797935.1_ASM979793v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:30,419] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:30,420] [INFO] Task started: HMMsearch
[2024-01-24 13:13:30,420] [INFO] Running command: hmmsearch --tblout GCF_009797935.1_ASM979793v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/reference_markers.hmm GCF_009797935.1_ASM979793v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:30,784] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:30,786] [INFO] Found 6/6 markers.
[2024-01-24 13:13:30,842] [INFO] Query marker FASTA was written to GCF_009797935.1_ASM979793v1_genomic.fna/markers.fasta
[2024-01-24 13:13:30,842] [INFO] Task started: Blastn
[2024-01-24 13:13:30,843] [INFO] Running command: blastn -query GCF_009797935.1_ASM979793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/reference_markers.fasta -out GCF_009797935.1_ASM979793v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:31,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:31,480] [INFO] Selected 23 target genomes.
[2024-01-24 13:13:31,480] [INFO] Target genome list was writen to GCF_009797935.1_ASM979793v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:31,493] [INFO] Task started: fastANI
[2024-01-24 13:13:31,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg91be0d62-78f6-4d44-bba0-271b73d2d22c/GCF_009797935.1_ASM979793v1_genomic.fna.gz --refList GCF_009797935.1_ASM979793v1_genomic.fna/target_genomes.txt --output GCF_009797935.1_ASM979793v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:51,550] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:51,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:51,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:51,569] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:51,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:51,569] [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
Lunatibacter salilacus	strain=CUG 91308	GCA_009797935.1	2483804	2483804	type	True	100.0	2232	2234	95	conclusive
Lunatimonas lonarensis	strain=AK24	GCA_000390185.1	1232681	1232681	type	True	77.1303	179	2234	95	below_threshold
Lunatimonas salinarum	strain=KCTC 42988	GCA_017811155.1	1774590	1774590	type	True	77.016	196	2234	95	below_threshold
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	76.9979	161	2234	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	76.9452	148	2234	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	76.7596	174	2234	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	76.6546	138	2234	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.6308	70	2234	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	76.5505	197	2234	95	below_threshold
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	76.5112	124	2234	95	below_threshold
Belliella kenyensis	strain=DSM 46651	GCA_022549675.1	1472724	1472724	type	True	76.5016	61	2234	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	76.3627	63	2234	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.1608	71	2234	95	below_threshold
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	76.1372	57	2234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:51,571] [INFO] DFAST Taxonomy check result was written to GCF_009797935.1_ASM979793v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:51,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:51,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:51,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/checkm_data
[2024-01-24 13:13:51,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:51,635] [INFO] Task started: CheckM
[2024-01-24 13:13:51,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009797935.1_ASM979793v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009797935.1_ASM979793v1_genomic.fna/checkm_input GCF_009797935.1_ASM979793v1_genomic.fna/checkm_result
[2024-01-24 13:15:17,266] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:17,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:17,299] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:17,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:17,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009797935.1_ASM979793v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:17,300] [INFO] Task started: Blastn
[2024-01-24 13:15:17,301] [INFO] Running command: blastn -query GCF_009797935.1_ASM979793v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd983e088-97e0-47c3-98fa-0b72bd200e4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009797935.1_ASM979793v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:18,147] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:18,152] [INFO] Selected 25 target genomes.
[2024-01-24 13:15:18,152] [INFO] Target genome list was writen to GCF_009797935.1_ASM979793v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:18,217] [INFO] Task started: fastANI
[2024-01-24 13:15:18,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg91be0d62-78f6-4d44-bba0-271b73d2d22c/GCF_009797935.1_ASM979793v1_genomic.fna.gz --refList GCF_009797935.1_ASM979793v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009797935.1_ASM979793v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:40,546] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:40,563] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:40,564] [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_009797935.1	s__Lunatimonas salilacus	100.0	2232	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016124425.1	s__Lunatimonas sp016124425	78.4626	483	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018500185.1	s__Litoribacter ruber	77.1054	60	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	98.60	98.60	0.91	0.91	2	-
GCF_017811155.1	s__Lunatimonas salinarum	77.039	195	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119245.1	s__Cyclobacterium sp010119245	76.9983	161	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	76.9439	148	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993705.1	s__Cyclobacterium sp010993705	76.835	175	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119225.1	s__Cyclobacterium sp010119225	76.7463	175	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009467825.1	s__Cyclobacterium xiamenense	76.6558	138	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCA_003565295.1	s__Negadavirga sp003565295	76.641	141	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Negadavirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143075.1	s__Cyclobacterium lianum	76.5439	122	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	76.5372	197	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762705.1	s__Cyclobacterium sp014762705	76.4502	180	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655305.1	s__Algoriphagus sp007655305	76.3627	63	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	76.3318	63	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113375.1	s__Algoriphagus hitonicola	76.1372	57	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	75.966	56	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126775.1	s__Cecembia sp007126775	75.7626	66	2234	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cecembia	95.0	99.59	99.59	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:40,566] [INFO] GTDB search result was written to GCF_009797935.1_ASM979793v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:40,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:40,570] [INFO] DFAST_QC result json was written to GCF_009797935.1_ASM979793v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:40,570] [INFO] DFAST_QC completed!
[2024-01-24 13:15:40,570] [INFO] Total running time: 0h2m45s