[2024-01-24 13:17:26,402] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:26,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:26,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference
[2024-01-24 13:17:27,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:27,617] [INFO] Task started: Prodigal
[2024-01-24 13:17:27,617] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd75cea4-3177-4856-95d9-fd5424b6d68a/GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/cds.fna -a GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,872] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,873] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,873] [INFO] Running command: hmmsearch --tblout GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/reference_markers.hmm GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:34,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:34,137] [INFO] Found 6/6 markers.
[2024-01-24 13:17:34,166] [INFO] Query marker FASTA was written to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:17:34,166] [INFO] Task started: Blastn
[2024-01-24 13:17:34,166] [INFO] Running command: blastn -query GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/reference_markers.fasta -out GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,772] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:34,773] [INFO] Target genome list was writen to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,782] [INFO] Task started: fastANI
[2024-01-24 13:17:34,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd75cea4-3177-4856-95d9-fd5424b6d68a/GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna.gz --refList GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:42,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:42,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:42,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:42,249] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:42,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:42,249] [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
Polynucleobacter kasalickyi	strain=VK13	GCA_900176405.1	1938817	1938817	type	True	100.0	949	951	95	conclusive
Polynucleobacter rarus	strain=MT-CBb6A5	GCA_003072505.1	556055	556055	type	True	80.3645	555	951	95	below_threshold
Polynucleobacter victoriensis	strain=MWH-VicM1	GCA_900187875.1	2049319	2049319	type	True	77.1383	55	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:42,251] [INFO] DFAST Taxonomy check result was written to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:17:42,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:42,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:42,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/checkm_data
[2024-01-24 13:17:42,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:42,284] [INFO] Task started: CheckM
[2024-01-24 13:17:42,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/checkm_input GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:18:08,147] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:08,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:08,161] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:08,161] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:08,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:18:08,162] [INFO] Task started: Blastn
[2024-01-24 13:18:08,162] [INFO] Running command: blastn -query GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5448eb76-9eed-48c4-a60b-3cab58dcf390/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:08,988] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:08,991] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:08,991] [INFO] Target genome list was writen to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:09,038] [INFO] Task started: fastANI
[2024-01-24 13:18:09,038] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd75cea4-3177-4856-95d9-fd5424b6d68a/GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna.gz --refList GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:16,239] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:16,251] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:16,251] [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_900176405.1	s__Polynucleobacter sp900176405	100.0	949	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.69	98.69	0.92	0.91	3	conclusive
GCF_003072505.1	s__Polynucleobacter rarus	80.3645	555	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889595.1	s__Polynucleobacter sp903889595	80.1326	432	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.49	99.49	0.84	0.84	2	-
GCA_903867305.1	s__Polynucleobacter sp903867305	77.1722	132	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.81	99.77	0.91	0.90	6	-
GCA_903821995.1	s__Polynucleobacter sp903821995	77.0421	70	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.83	99.77	0.91	0.85	9	-
GCA_903875135.1	s__Polynucleobacter sp903875135	76.741	118	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.93	99.91	0.96	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:16,253] [INFO] GTDB search result was written to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:16,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:16,256] [INFO] DFAST_QC result json was written to GCF_900176405.1_IMG-taxon_2708742530_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:18:16,256] [INFO] DFAST_QC completed!
[2024-01-24 13:18:16,256] [INFO] Total running time: 0h0m50s