[2024-01-24 13:01:04,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:04,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:04,157] [INFO] DQC Reference Directory: /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference
[2024-01-24 13:01:06,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:06,817] [INFO] Task started: Prodigal
[2024-01-24 13:01:06,817] [INFO] Running command: gunzip -c /var/lib/cwl/stgb22ead66-4d4d-4cda-bb11-7436bde0d819/GCF_003721565.1_ASM372156v1_genomic.fna.gz | prodigal -d GCF_003721565.1_ASM372156v1_genomic.fna/cds.fna -a GCF_003721565.1_ASM372156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:33,672] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:33,672] [INFO] Task started: HMMsearch
[2024-01-24 13:01:33,672] [INFO] Running command: hmmsearch --tblout GCF_003721565.1_ASM372156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/reference_markers.hmm GCF_003721565.1_ASM372156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:34,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:34,021] [INFO] Found 6/6 markers.
[2024-01-24 13:01:34,061] [INFO] Query marker FASTA was written to GCF_003721565.1_ASM372156v1_genomic.fna/markers.fasta
[2024-01-24 13:01:34,062] [INFO] Task started: Blastn
[2024-01-24 13:01:34,062] [INFO] Running command: blastn -query GCF_003721565.1_ASM372156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/reference_markers.fasta -out GCF_003721565.1_ASM372156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:34,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:34,700] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:34,700] [INFO] Target genome list was writen to GCF_003721565.1_ASM372156v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:34,710] [INFO] Task started: fastANI
[2024-01-24 13:01:34,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ead66-4d4d-4cda-bb11-7436bde0d819/GCF_003721565.1_ASM372156v1_genomic.fna.gz --refList GCF_003721565.1_ASM372156v1_genomic.fna/target_genomes.txt --output GCF_003721565.1_ASM372156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:47,810] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:47,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:47,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:47,821] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:47,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:47,821] [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 immobilis	strain=MCC P1	GCA_003721565.1	1348778	1348778	type	True	100.0	1585	1585	95	conclusive
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	82.4387	1014	1585	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	82.3828	1039	1585	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	81.2884	962	1585	95	below_threshold
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	80.9705	927	1585	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	80.9376	927	1585	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	80.6384	874	1585	95	below_threshold
Rufibacter radiotolerans	strain=DG31D	GCA_001078055.1	1379910	1379910	type	True	80.411	801	1585	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	79.8516	784	1585	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	76.757	124	1585	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	76.2226	71	1585	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	75.9487	99	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:47,823] [INFO] DFAST Taxonomy check result was written to GCF_003721565.1_ASM372156v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:47,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:47,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:47,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/checkm_data
[2024-01-24 13:01:47,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:47,869] [INFO] Task started: CheckM
[2024-01-24 13:01:47,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721565.1_ASM372156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721565.1_ASM372156v1_genomic.fna/checkm_input GCF_003721565.1_ASM372156v1_genomic.fna/checkm_result
[2024-01-24 13:02:59,318] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:59,319] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:59,342] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:59,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:59,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721565.1_ASM372156v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:59,343] [INFO] Task started: Blastn
[2024-01-24 13:02:59,343] [INFO] Running command: blastn -query GCF_003721565.1_ASM372156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg588722f5-622c-4407-a571-151c444de611/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721565.1_ASM372156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:00,109] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:00,113] [INFO] Selected 11 target genomes.
[2024-01-24 13:03:00,114] [INFO] Target genome list was writen to GCF_003721565.1_ASM372156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:00,124] [INFO] Task started: fastANI
[2024-01-24 13:03:00,124] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22ead66-4d4d-4cda-bb11-7436bde0d819/GCF_003721565.1_ASM372156v1_genomic.fna.gz --refList GCF_003721565.1_ASM372156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721565.1_ASM372156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:13,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:13,588] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:13,589] [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_003721565.1	s__Rufibacter immobilis	100.0	1585	1585	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_014269285.1	s__Rufibacter sediminis	82.4034	1036	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647275.1	s__Rufibacter ruber	81.7962	860	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	98.26	98.26	0.93	0.93	2	-
GCF_016924645.1	s__Rufibacter sp016924645	81.6869	988	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271695.1	s__Rufibacter sp008271695	81.2815	963	1585	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	81.1144	941	1585	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	81.1016	967	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271745.1	s__Rufibacter glacialis	80.9472	925	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017916365.1	s__Rufibacter sp017916365	80.9167	942	1585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_003721515.1	s__Rufibacter latericius	80.6522	872	1585	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	80.4112	801	1585	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 13:03:13,591] [INFO] GTDB search result was written to GCF_003721565.1_ASM372156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:13,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:13,594] [INFO] DFAST_QC result json was written to GCF_003721565.1_ASM372156v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:13,594] [INFO] DFAST_QC completed!
[2024-01-24 13:03:13,594] [INFO] Total running time: 0h2m9s