[2024-01-24 13:10:04,024] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:04,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:04,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference
[2024-01-24 13:10:05,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,341] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b97423f-f302-4f27-83d6-93304e97dde2/GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/cds.fna -a GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:11,115] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:11,116] [INFO] Task started: HMMsearch
[2024-01-24 13:10:11,116] [INFO] Running command: hmmsearch --tblout GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/reference_markers.hmm GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:11,399] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:11,401] [INFO] Found 6/6 markers.
[2024-01-24 13:10:11,418] [INFO] Query marker FASTA was written to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:11,418] [INFO] Task started: Blastn
[2024-01-24 13:10:11,419] [INFO] Running command: blastn -query GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/reference_markers.fasta -out GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,990] [INFO] Selected 8 target genomes.
[2024-01-24 13:10:11,991] [INFO] Target genome list was writen to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:11,995] [INFO] Task started: fastANI
[2024-01-24 13:10:11,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b97423f-f302-4f27-83d6-93304e97dde2/GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna.gz --refList GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:15,435] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:15,436] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:15,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:15,444] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:15,444] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:15,444] [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
Thermocrinis minervae	strain=DSM 19557	GCA_900142435.1	381751	381751	type	True	100.0	455	455	95	conclusive
Hydrogenobacter hydrogenophilus	strain=DSM 2913	GCA_900215655.1	35835	35835	type	True	77.5438	58	455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,446] [INFO] DFAST Taxonomy check result was written to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:15,447] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:15,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:15,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/checkm_data
[2024-01-24 13:10:15,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:15,466] [INFO] Task started: CheckM
[2024-01-24 13:10:15,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/checkm_input GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:39,032] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:39,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:39,053] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:39,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:39,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:39,055] [INFO] Task started: Blastn
[2024-01-24 13:10:39,055] [INFO] Running command: blastn -query GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg528ed306-3cbe-4dfa-82d7-6e4a96885c82/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:39,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:39,813] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:39,813] [INFO] Target genome list was writen to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:39,828] [INFO] Task started: fastANI
[2024-01-24 13:10:39,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b97423f-f302-4f27-83d6-93304e97dde2/GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna.gz --refList GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:45,132] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:45,141] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:45,142] [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_900142435.1	s__Thermocrinis_A minervae	100.0	455	455	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Thermocrinis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900215655.1	s__Hydrogenobacter hydrogenophilus	77.5438	58	455	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__Hydrogenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018771605.1	s__UBA11096 sp003534055	76.7848	65	455	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	98.57	98.52	0.97	0.96	3	-
GCA_011054805.1	s__UBA11096 sp011054805	76.5368	57	455	d__Bacteria;p__Aquificota;c__Aquificae;o__Aquificales;f__Aquificaceae;g__UBA11096	95.0	99.69	99.59	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:45,143] [INFO] GTDB search result was written to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:45,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:45,146] [INFO] DFAST_QC result json was written to GCF_900142435.1_IMG-taxon_2698536703_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:10:45,146] [INFO] DFAST_QC completed!
[2024-01-24 13:10:45,147] [INFO] Total running time: 0h0m41s