[2024-01-24 13:32:18,355] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference
[2024-01-24 13:32:19,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,652] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg3312f578-4063-4517-9824-e53548fae2fa/GCF_001078055.1_ASM107805v1_genomic.fna.gz | prodigal -d GCF_001078055.1_ASM107805v1_genomic.fna/cds.fna -a GCF_001078055.1_ASM107805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,750] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,751] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,751] [INFO] Running command: hmmsearch --tblout GCF_001078055.1_ASM107805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/reference_markers.hmm GCF_001078055.1_ASM107805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:48,081] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:48,083] [INFO] Found 6/6 markers.
[2024-01-24 13:32:48,124] [INFO] Query marker FASTA was written to GCF_001078055.1_ASM107805v1_genomic.fna/markers.fasta
[2024-01-24 13:32:48,125] [INFO] Task started: Blastn
[2024-01-24 13:32:48,125] [INFO] Running command: blastn -query GCF_001078055.1_ASM107805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/reference_markers.fasta -out GCF_001078055.1_ASM107805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,745] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,748] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:48,748] [INFO] Target genome list was writen to GCF_001078055.1_ASM107805v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:48,753] [INFO] Task started: fastANI
[2024-01-24 13:32:48,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg3312f578-4063-4517-9824-e53548fae2fa/GCF_001078055.1_ASM107805v1_genomic.fna.gz --refList GCF_001078055.1_ASM107805v1_genomic.fna/target_genomes.txt --output GCF_001078055.1_ASM107805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:02,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:02,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:02,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:02,148] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:02,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:02,149] [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
Rufibacter radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	100.0	1606	1606	95	conclusive
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	80.5345	888	1606	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	80.4838	904	1606	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	80.404	858	1606	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	80.2672	857	1606	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	80.2522	880	1606	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	79.9906	805	1606	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	79.5129	700	1606	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	76.7492	212	1606	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	76.5569	101	1606	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	76.3238	179	1606	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:02,150] [INFO] DFAST Taxonomy check result was written to GCF_001078055.1_ASM107805v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:02,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:02,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:02,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/checkm_data
[2024-01-24 13:33:02,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:02,199] [INFO] Task started: CheckM
[2024-01-24 13:33:02,199] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001078055.1_ASM107805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001078055.1_ASM107805v1_genomic.fna/checkm_input GCF_001078055.1_ASM107805v1_genomic.fna/checkm_result
[2024-01-24 13:34:13,495] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:13,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:13,517] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:13,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:13,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001078055.1_ASM107805v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:13,518] [INFO] Task started: Blastn
[2024-01-24 13:34:13,519] [INFO] Running command: blastn -query GCF_001078055.1_ASM107805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf9774b6-0768-4421-abe2-bf8ee1561450/dqc_reference/reference_markers_gtdb.fasta -out GCF_001078055.1_ASM107805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:14,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:14,372] [INFO] Selected 12 target genomes.
[2024-01-24 13:34:14,372] [INFO] Target genome list was writen to GCF_001078055.1_ASM107805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:14,387] [INFO] Task started: fastANI
[2024-01-24 13:34:14,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg3312f578-4063-4517-9824-e53548fae2fa/GCF_001078055.1_ASM107805v1_genomic.fna.gz --refList GCF_001078055.1_ASM107805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001078055.1_ASM107805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:28,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:28,474] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:28,474] [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_001078055.1	s__Rufibacter radiotolerans	100.0	1606	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008271745.1	s__Rufibacter glacialis	80.4776	904	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008271695.1	s__Rufibacter sp008271695	80.4084	857	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916365.1	s__Rufibacter sp017916365	80.3618	865	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_014269285.1	s__Rufibacter sediminis	80.269	858	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924645.1	s__Rufibacter sp016924645	80.2148	896	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721565.1	s__Rufibacter immobilis	80.1917	809	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623775.1	s__Rufibacter sp013623775	80.1478	837	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721515.1	s__Rufibacter latericius	79.9878	807	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355955.1	s__Rufibacter sp017355955	79.9431	808	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913235.1	s__Nibribacter ruber	79.7098	674	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310085.1	s__Rufibacter tibetensis	79.5022	701	1606	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:28,476] [INFO] GTDB search result was written to GCF_001078055.1_ASM107805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:28,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:28,485] [INFO] DFAST_QC result json was written to GCF_001078055.1_ASM107805v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:28,485] [INFO] DFAST_QC completed!
[2024-01-24 13:34:28,486] [INFO] Total running time: 0h2m10s