[2024-01-24 13:28:25,622] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,623] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,624] [INFO] DQC Reference Directory: /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference
[2024-01-24 13:28:26,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:26,895] [INFO] Task started: Prodigal
[2024-01-24 13:28:26,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg46d13feb-0e1f-46c8-abfb-d28e50ad8745/GCF_008271745.1_ASM827174v1_genomic.fna.gz | prodigal -d GCF_008271745.1_ASM827174v1_genomic.fna/cds.fna -a GCF_008271745.1_ASM827174v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:57,771] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:57,771] [INFO] Task started: HMMsearch
[2024-01-24 13:28:57,772] [INFO] Running command: hmmsearch --tblout GCF_008271745.1_ASM827174v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/reference_markers.hmm GCF_008271745.1_ASM827174v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:58,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:58,053] [INFO] Found 6/6 markers.
[2024-01-24 13:28:58,097] [INFO] Query marker FASTA was written to GCF_008271745.1_ASM827174v1_genomic.fna/markers.fasta
[2024-01-24 13:28:58,098] [INFO] Task started: Blastn
[2024-01-24 13:28:58,098] [INFO] Running command: blastn -query GCF_008271745.1_ASM827174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/reference_markers.fasta -out GCF_008271745.1_ASM827174v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:58,717] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:58,721] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:58,721] [INFO] Target genome list was writen to GCF_008271745.1_ASM827174v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:58,731] [INFO] Task started: fastANI
[2024-01-24 13:28:58,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d13feb-0e1f-46c8-abfb-d28e50ad8745/GCF_008271745.1_ASM827174v1_genomic.fna.gz --refList GCF_008271745.1_ASM827174v1_genomic.fna/target_genomes.txt --output GCF_008271745.1_ASM827174v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:11,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:11,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:11,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:11,591] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:11,591] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:11,591] [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 glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	100.0	1763	1763	95	conclusive
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	99.9982	1756	1763	95	conclusive
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	81.7718	1054	1763	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	81.7443	1042	1763	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	81.3525	1015	1763	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	80.9316	990	1763	95	below_threshold
Rufibacter immobilis	strain=MCC P1	GCA_003721565.1	1348778	1348778	type	True	80.8822	937	1763	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	80.7735	978	1763	95	below_threshold
Rufibacter radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	80.6087	883	1763	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	76.7913	193	1763	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	76.4033	157	1763	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	76.1726	80	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:11,593] [INFO] DFAST Taxonomy check result was written to GCF_008271745.1_ASM827174v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:11,593] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:11,594] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:11,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/checkm_data
[2024-01-24 13:29:11,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:11,651] [INFO] Task started: CheckM
[2024-01-24 13:29:11,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008271745.1_ASM827174v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008271745.1_ASM827174v1_genomic.fna/checkm_input GCF_008271745.1_ASM827174v1_genomic.fna/checkm_result
[2024-01-24 13:30:30,350] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:30,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:30,370] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:30,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:30,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008271745.1_ASM827174v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:30,371] [INFO] Task started: Blastn
[2024-01-24 13:30:30,371] [INFO] Running command: blastn -query GCF_008271745.1_ASM827174v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg483e7d22-8fad-4ea3-b21e-87d9b5bc8daa/dqc_reference/reference_markers_gtdb.fasta -out GCF_008271745.1_ASM827174v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:31,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:31,185] [INFO] Selected 12 target genomes.
[2024-01-24 13:30:31,185] [INFO] Target genome list was writen to GCF_008271745.1_ASM827174v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:31,197] [INFO] Task started: fastANI
[2024-01-24 13:30:31,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg46d13feb-0e1f-46c8-abfb-d28e50ad8745/GCF_008271745.1_ASM827174v1_genomic.fna.gz --refList GCF_008271745.1_ASM827174v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008271745.1_ASM827174v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:46,192] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:46,206] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:46,206] [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_008271745.1	s__Rufibacter glacialis	100.0	1763	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014269285.1	s__Rufibacter sediminis	81.7261	1046	1763	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	81.6901	1007	1763	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	81.3684	1023	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_008271695.1	s__Rufibacter sp008271695	81.3528	1013	1763	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	81.0391	973	1763	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	80.9094	994	1763	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	80.8715	939	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310085.1	s__Rufibacter tibetensis	80.7784	976	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078055.1	s__Rufibacter radiotolerans	80.6317	880	1763	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	80.4081	970	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647285.1	s__Rufibacter roseus	78.7453	500	1763	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 13:30:46,208] [INFO] GTDB search result was written to GCF_008271745.1_ASM827174v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:46,208] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:46,211] [INFO] DFAST_QC result json was written to GCF_008271745.1_ASM827174v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:46,212] [INFO] DFAST_QC completed!
[2024-01-24 13:30:46,212] [INFO] Total running time: 0h2m21s