[2024-01-24 12:13:28,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:28,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:28,080] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference
[2024-01-24 12:13:29,452] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:29,453] [INFO] Task started: Prodigal
[2024-01-24 12:13:29,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgda2b3c89-0f66-44d0-b32b-a2d446a256c1/GCF_030409895.1_ASM3040989v1_genomic.fna.gz | prodigal -d GCF_030409895.1_ASM3040989v1_genomic.fna/cds.fna -a GCF_030409895.1_ASM3040989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:58,365] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:58,365] [INFO] Task started: HMMsearch
[2024-01-24 12:13:58,365] [INFO] Running command: hmmsearch --tblout GCF_030409895.1_ASM3040989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/reference_markers.hmm GCF_030409895.1_ASM3040989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:58,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:58,682] [INFO] Found 6/6 markers.
[2024-01-24 12:13:58,737] [INFO] Query marker FASTA was written to GCF_030409895.1_ASM3040989v1_genomic.fna/markers.fasta
[2024-01-24 12:13:58,737] [INFO] Task started: Blastn
[2024-01-24 12:13:58,738] [INFO] Running command: blastn -query GCF_030409895.1_ASM3040989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/reference_markers.fasta -out GCF_030409895.1_ASM3040989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:59,362] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:59,365] [INFO] Selected 11 target genomes.
[2024-01-24 12:13:59,365] [INFO] Target genome list was writen to GCF_030409895.1_ASM3040989v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:59,371] [INFO] Task started: fastANI
[2024-01-24 12:13:59,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2b3c89-0f66-44d0-b32b-a2d446a256c1/GCF_030409895.1_ASM3040989v1_genomic.fna.gz --refList GCF_030409895.1_ASM3040989v1_genomic.fna/target_genomes.txt --output GCF_030409895.1_ASM3040989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:12,360] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:12,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:12,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:12,369] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:12,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:12,370] [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 jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	99.9991	1903	1911	95	conclusive
Cyclobacterium salsum	strain=SYSU L10167	GCA_010119245.1	2666329	2666329	type	True	86.3282	1505	1911	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	86.0451	1470	1911	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	80.0529	760	1911	95	below_threshold
Cyclobacterium xiamenense	strain=CGMCC 1.12432	GCA_009467825.1	1297121	1297121	type	True	79.5911	797	1911	95	below_threshold
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	77.1262	257	1911	95	below_threshold
Lunatimonas salinarum	strain=KCTC 42988	GCA_017811155.1	1774590	1774590	type	True	76.2101	138	1911	95	below_threshold
Echinicola salinicaeni	strain=P51	GCA_014280965.1	2762757	2762757	type	True	75.4545	72	1911	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:12,371] [INFO] DFAST Taxonomy check result was written to GCF_030409895.1_ASM3040989v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:12,371] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:12,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:12,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/checkm_data
[2024-01-24 12:14:12,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:12,432] [INFO] Task started: CheckM
[2024-01-24 12:14:12,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409895.1_ASM3040989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409895.1_ASM3040989v1_genomic.fna/checkm_input GCF_030409895.1_ASM3040989v1_genomic.fna/checkm_result
[2024-01-24 12:15:30,985] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:30,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:31,009] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:31,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:31,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409895.1_ASM3040989v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:31,010] [INFO] Task started: Blastn
[2024-01-24 12:15:31,010] [INFO] Running command: blastn -query GCF_030409895.1_ASM3040989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd1fe6b5-e6ff-4d07-8f56-ee9b786fbd94/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409895.1_ASM3040989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,869] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:31,871] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:31,872] [INFO] Target genome list was writen to GCF_030409895.1_ASM3040989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:31,880] [INFO] Task started: fastANI
[2024-01-24 12:15:31,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2b3c89-0f66-44d0-b32b-a2d446a256c1/GCF_030409895.1_ASM3040989v1_genomic.fna.gz --refList GCF_030409895.1_ASM3040989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409895.1_ASM3040989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:44,452] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:44,465] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:44,465] [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_010994275.1	s__Cyclobacterium jeungdonense	99.9991	1903	1911	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_010119245.1	s__Cyclobacterium sp010119245	86.3317	1505	1911	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	86.0486	1469	1911	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	80.1198	773	1911	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	80.0617	758	1911	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	80.0221	729	1911	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	79.5849	798	1911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	97.69	97.69	0.89	0.89	2	-
GCF_000222485.1	s__Cyclobacterium marinum	77.127	256	1911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	-
GCF_017811155.1	s__Lunatimonas salinarum	76.2101	138	1911	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Lunatimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:44,467] [INFO] GTDB search result was written to GCF_030409895.1_ASM3040989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:44,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:44,470] [INFO] DFAST_QC result json was written to GCF_030409895.1_ASM3040989v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:44,470] [INFO] DFAST_QC completed!
[2024-01-24 12:15:44,470] [INFO] Total running time: 0h2m16s