[2024-01-25 18:48:35,861] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,862] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,862] [INFO] DQC Reference Directory: /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference
[2024-01-25 18:48:37,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:37,033] [INFO] Task started: Prodigal
[2024-01-25 18:48:37,034] [INFO] Running command: gunzip -c /var/lib/cwl/stg84bd4c02-75d4-44ce-9f81-3f9ee5936e23/GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/cds.fna -a GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:59,276] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:59,276] [INFO] Task started: HMMsearch
[2024-01-25 18:48:59,276] [INFO] Running command: hmmsearch --tblout GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/reference_markers.hmm GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:59,502] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:59,503] [INFO] Found 6/6 markers.
[2024-01-25 18:48:59,543] [INFO] Query marker FASTA was written to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:48:59,543] [INFO] Task started: Blastn
[2024-01-25 18:48:59,543] [INFO] Running command: blastn -query GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/reference_markers.fasta -out GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:00,147] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:00,150] [INFO] Selected 11 target genomes.
[2024-01-25 18:49:00,151] [INFO] Target genome list was writen to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:49:00,165] [INFO] Task started: fastANI
[2024-01-25 18:49:00,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg84bd4c02-75d4-44ce-9f81-3f9ee5936e23/GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna.gz --refList GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:13,759] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:13,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:13,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:13,767] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:13,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:13,767] [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 chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	100.0	1674	1676	95	conclusive
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	92.0328	1473	1676	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	83.3023	1166	1676	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	81.6894	997	1676	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	80.16	806	1676	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	79.4579	630	1676	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	79.1466	741	1676	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.56	601	1676	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.96	481	1676	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.9254	362	1676	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.6737	201	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:13,769] [INFO] DFAST Taxonomy check result was written to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:49:13,769] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:13,769] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:13,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/checkm_data
[2024-01-25 18:49:13,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:13,819] [INFO] Task started: CheckM
[2024-01-25 18:49:13,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/checkm_input GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:50:12,360] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:12,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:12,382] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:12,382] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:12,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:50:12,384] [INFO] Task started: Blastn
[2024-01-25 18:50:12,384] [INFO] Running command: blastn -query GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg56962c02-bc7c-48d3-bf3e-66ff2faec147/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:13,237] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:13,240] [INFO] Selected 7 target genomes.
[2024-01-25 18:50:13,240] [INFO] Target genome list was writen to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:13,247] [INFO] Task started: fastANI
[2024-01-25 18:50:13,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg84bd4c02-75d4-44ce-9f81-3f9ee5936e23/GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna.gz --refList GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:24,917] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:24,923] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:24,923] [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_900113285.1	s__Pontibacter chinhatensis	100.0	1674	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003054055.1	s__Pontibacter mucosus	92.0227	1474	1676	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	83.3249	1162	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385705.1	s__Pontibacter sp006385705	81.7423	988	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	80.1765	802	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576375.1	s__Pontibacter oryzae	79.4581	629	1676	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	79.1399	744	1676	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:24,924] [INFO] GTDB search result was written to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:24,925] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:24,929] [INFO] DFAST_QC result json was written to GCF_900113285.1_IMG-taxon_2671180224_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:50:24,929] [INFO] DFAST_QC completed!
[2024-01-25 18:50:24,929] [INFO] Total running time: 0h1m49s