[2024-01-24 13:17:01,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:01,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:01,970] [INFO] DQC Reference Directory: /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference
[2024-01-24 13:17:03,216] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:03,217] [INFO] Task started: Prodigal
[2024-01-24 13:17:03,217] [INFO] Running command: gunzip -c /var/lib/cwl/stg20b99fa7-b9cf-42a9-8059-fe5332d68f70/GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/cds.fna -a GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,568] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,568] [INFO] Running command: hmmsearch --tblout GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/reference_markers.hmm GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,991] [INFO] Found 6/6 markers.
[2024-01-24 13:17:34,050] [INFO] Query marker FASTA was written to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:34,051] [INFO] Task started: Blastn
[2024-01-24 13:17:34,051] [INFO] Running command: blastn -query GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/reference_markers.fasta -out GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,718] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:34,719] [INFO] Target genome list was writen to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,725] [INFO] Task started: fastANI
[2024-01-24 13:17:34,725] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b99fa7-b9cf-42a9-8059-fe5332d68f70/GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna.gz --refList GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:46,956] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:46,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:46,977] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:46,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:46,978] [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
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	100.0	1945	1948	95	conclusive
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	99.9983	1942	1948	95	conclusive
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	79.3077	629	1948	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	79.2197	635	1948	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.9022	569	1948	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.6488	549	1948	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	78.5339	468	1948	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.5187	498	1948	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	78.4443	535	1948	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.3241	422	1948	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	78.0223	323	1948	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.7551	288	1948	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.5014	285	1948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,979] [INFO] DFAST Taxonomy check result was written to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:46,980] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:46,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:46,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/checkm_data
[2024-01-24 13:17:46,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:47,055] [INFO] Task started: CheckM
[2024-01-24 13:17:47,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/checkm_input GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:19:02,972] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:02,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:02,993] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:02,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:02,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:19:02,994] [INFO] Task started: Blastn
[2024-01-24 13:19:02,994] [INFO] Running command: blastn -query GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8f5ed79-61cf-47da-9c50-0faf17123216/dqc_reference/reference_markers_gtdb.fasta -out GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,755] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,758] [INFO] Selected 12 target genomes.
[2024-01-24 13:19:03,758] [INFO] Target genome list was writen to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:03,782] [INFO] Task started: fastANI
[2024-01-24 13:19:03,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b99fa7-b9cf-42a9-8059-fe5332d68f70/GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna.gz --refList GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:15,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:15,425] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:15,425] [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_900188175.1	s__Pontibacter ummariensis	100.0	1945	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003585765.1	s__Pontibacter actiniarum	79.3044	630	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385705.1	s__Pontibacter sp006385705	78.8818	572	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054055.1	s__Pontibacter mucosus	78.6559	547	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973725.1	s__Pontibacter korlensis	78.5444	468	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.5134	498	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	78.4443	535	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	78.4338	512	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003367245.1	s__Pontibacter diazotrophicus	78.3634	602	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576375.1	s__Pontibacter oryzae	78.3548	425	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931655.1	s__Pontibacter russatus	78.168	514	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014306105.1	s__Pontibacter sp014306105	78.1332	383	1948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,427] [INFO] GTDB search result was written to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:15,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:15,431] [INFO] DFAST_QC result json was written to GCF_900188175.1_IMG-taxon_2706794922_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:19:15,431] [INFO] DFAST_QC completed!
[2024-01-24 13:19:15,431] [INFO] Total running time: 0h2m13s