[2024-01-24 14:53:50,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference
[2024-01-24 14:53:51,456] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,457] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,457] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8d7508b-f281-45b0-a9d7-81aef3c68806/GCF_010119245.1_ASM1011924v1_genomic.fna.gz | prodigal -d GCF_010119245.1_ASM1011924v1_genomic.fna/cds.fna -a GCF_010119245.1_ASM1011924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:19,821] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:19,822] [INFO] Task started: HMMsearch
[2024-01-24 14:54:19,822] [INFO] Running command: hmmsearch --tblout GCF_010119245.1_ASM1011924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/reference_markers.hmm GCF_010119245.1_ASM1011924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:20,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:20,131] [INFO] Found 6/6 markers.
[2024-01-24 14:54:20,182] [INFO] Query marker FASTA was written to GCF_010119245.1_ASM1011924v1_genomic.fna/markers.fasta
[2024-01-24 14:54:20,182] [INFO] Task started: Blastn
[2024-01-24 14:54:20,182] [INFO] Running command: blastn -query GCF_010119245.1_ASM1011924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/reference_markers.fasta -out GCF_010119245.1_ASM1011924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:20,776] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:20,781] [INFO] Selected 11 target genomes.
[2024-01-24 14:54:20,781] [INFO] Target genome list was writen to GCF_010119245.1_ASM1011924v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:20,787] [INFO] Task started: fastANI
[2024-01-24 14:54:20,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d7508b-f281-45b0-a9d7-81aef3c68806/GCF_010119245.1_ASM1011924v1_genomic.fna.gz --refList GCF_010119245.1_ASM1011924v1_genomic.fna/target_genomes.txt --output GCF_010119245.1_ASM1011924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:32,557] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:32,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:32,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:32,569] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:32,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:32,569] [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
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	100.0	1932	1934	95	conclusive
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	94.0728	1627	1934	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	86.2517	1518	1934	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	80.4419	750	1934	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	80.3816	840	1934	95	below_threshold
Cyclobacterium lianum	strain=CGMCC 1.6102	GCA_900143075.1	388280	388280	type	True	78.7774	588	1934	95	below_threshold
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	77.385	224	1934	95	below_threshold
Cecembia lonarensis	strain=LW9	GCA_000298295.1	645110	645110	type	True	76.4721	62	1934	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	76.2786	65	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:32,571] [INFO] DFAST Taxonomy check result was written to GCF_010119245.1_ASM1011924v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:32,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:32,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:32,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/checkm_data
[2024-01-24 14:54:32,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:32,629] [INFO] Task started: CheckM
[2024-01-24 14:54:32,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119245.1_ASM1011924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119245.1_ASM1011924v1_genomic.fna/checkm_input GCF_010119245.1_ASM1011924v1_genomic.fna/checkm_result
[2024-01-24 14:55:49,051] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:49,052] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:49,081] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:49,082] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:49,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119245.1_ASM1011924v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:49,083] [INFO] Task started: Blastn
[2024-01-24 14:55:49,083] [INFO] Running command: blastn -query GCF_010119245.1_ASM1011924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5bc8b3b-0423-4be7-9093-fb40455d937f/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119245.1_ASM1011924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:49,809] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:49,812] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:49,812] [INFO] Target genome list was writen to GCF_010119245.1_ASM1011924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:49,826] [INFO] Task started: fastANI
[2024-01-24 14:55:49,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d7508b-f281-45b0-a9d7-81aef3c68806/GCF_010119245.1_ASM1011924v1_genomic.fna.gz --refList GCF_010119245.1_ASM1011924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119245.1_ASM1011924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:02,122] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:02,135] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:02,135] [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_010119245.1	s__Cyclobacterium sp010119245	100.0	1932	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010119225.1	s__Cyclobacterium sp010119225	94.0642	1628	1934	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	86.2414	1520	1934	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	82.81	868	1934	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	80.438	751	1934	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	80.3782	841	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCA_014762705.1	s__Cyclobacterium sp014762705	79.7131	759	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222485.1	s__Cyclobacterium marinum	77.385	224	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	-
GCF_000295935.2	s__Indibacter alkaliphilus	76.4663	66	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Indibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280965.1	s__Echinicola sp014280965	76.2786	65	1934	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:02,138] [INFO] GTDB search result was written to GCF_010119245.1_ASM1011924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:02,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:02,142] [INFO] DFAST_QC result json was written to GCF_010119245.1_ASM1011924v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:02,142] [INFO] DFAST_QC completed!
[2024-01-24 14:56:02,143] [INFO] Total running time: 0h2m12s