[2024-01-25 18:11:50,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:50,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:50,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference
[2024-01-25 18:11:51,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:51,816] [INFO] Task started: Prodigal
[2024-01-25 18:11:51,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg64200b2d-ee0c-4342-ae52-d0ea07e72065/GCF_003721515.1_ASM372151v1_genomic.fna.gz | prodigal -d GCF_003721515.1_ASM372151v1_genomic.fna/cds.fna -a GCF_003721515.1_ASM372151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:18,223] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:18,223] [INFO] Task started: HMMsearch
[2024-01-25 18:12:18,224] [INFO] Running command: hmmsearch --tblout GCF_003721515.1_ASM372151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/reference_markers.hmm GCF_003721515.1_ASM372151v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:18,508] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:18,509] [INFO] Found 6/6 markers.
[2024-01-25 18:12:18,555] [INFO] Query marker FASTA was written to GCF_003721515.1_ASM372151v1_genomic.fna/markers.fasta
[2024-01-25 18:12:18,556] [INFO] Task started: Blastn
[2024-01-25 18:12:18,556] [INFO] Running command: blastn -query GCF_003721515.1_ASM372151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/reference_markers.fasta -out GCF_003721515.1_ASM372151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:19,117] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:19,119] [INFO] Selected 10 target genomes.
[2024-01-25 18:12:19,120] [INFO] Target genome list was writen to GCF_003721515.1_ASM372151v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:19,147] [INFO] Task started: fastANI
[2024-01-25 18:12:19,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg64200b2d-ee0c-4342-ae52-d0ea07e72065/GCF_003721515.1_ASM372151v1_genomic.fna.gz --refList GCF_003721515.1_ASM372151v1_genomic.fna/target_genomes.txt --output GCF_003721515.1_ASM372151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:30,596] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:30,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:30,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:30,604] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:30,605] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:30,605] [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 latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	100.0	1879	1879	95	conclusive
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	83.5053	1333	1879	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	83.3905	1291	1879	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	83.3551	1292	1879	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	81.5707	963	1879	95	below_threshold
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	81.0853	980	1879	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	81.0392	987	1879	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	76.6187	164	1879	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.2806	101	1879	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	76.1675	99	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,606] [INFO] DFAST Taxonomy check result was written to GCF_003721515.1_ASM372151v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:30,606] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:30,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:30,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/checkm_data
[2024-01-25 18:12:30,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:30,662] [INFO] Task started: CheckM
[2024-01-25 18:12:30,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721515.1_ASM372151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721515.1_ASM372151v1_genomic.fna/checkm_input GCF_003721515.1_ASM372151v1_genomic.fna/checkm_result
[2024-01-25 18:13:39,882] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:39,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:39,918] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:39,918] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:39,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721515.1_ASM372151v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:39,920] [INFO] Task started: Blastn
[2024-01-25 18:13:39,920] [INFO] Running command: blastn -query GCF_003721515.1_ASM372151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fd2aa17-648d-42c4-aa5b-8ffb57940758/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721515.1_ASM372151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:40,779] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:40,782] [INFO] Selected 7 target genomes.
[2024-01-25 18:13:40,782] [INFO] Target genome list was writen to GCF_003721515.1_ASM372151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:40,789] [INFO] Task started: fastANI
[2024-01-25 18:13:40,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg64200b2d-ee0c-4342-ae52-d0ea07e72065/GCF_003721515.1_ASM372151v1_genomic.fna.gz --refList GCF_003721515.1_ASM372151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721515.1_ASM372151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:50,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:50,494] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:50,495] [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_003721515.1	s__Rufibacter latericius	100.0	1879	1879	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_008271695.1	s__Rufibacter sp008271695	83.5085	1332	1879	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	83.3891	1307	1879	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	83.3602	1291	1879	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	82.1825	1056	1879	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	81.5853	961	1879	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	81.0194	991	1879	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:50,496] [INFO] GTDB search result was written to GCF_003721515.1_ASM372151v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:50,497] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:50,499] [INFO] DFAST_QC result json was written to GCF_003721515.1_ASM372151v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:50,499] [INFO] DFAST_QC completed!
[2024-01-25 18:13:50,499] [INFO] Total running time: 0h1m60s