[2024-01-24 12:06:24,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference
[2024-01-24 12:06:25,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,939] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg80f3af67-423d-4eb1-8e3d-a7e91faf1c0a/GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/cds.fna -a GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:52,677] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:52,677] [INFO] Task started: HMMsearch
[2024-01-24 12:06:52,677] [INFO] Running command: hmmsearch --tblout GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/reference_markers.hmm GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:53,036] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:53,038] [INFO] Found 6/6 markers.
[2024-01-24 12:06:53,115] [INFO] Query marker FASTA was written to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:06:53,115] [INFO] Task started: Blastn
[2024-01-24 12:06:53,115] [INFO] Running command: blastn -query GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/reference_markers.fasta -out GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:54,404] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:54,408] [INFO] Selected 7 target genomes.
[2024-01-24 12:06:54,409] [INFO] Target genome list was writen to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:06:54,412] [INFO] Task started: fastANI
[2024-01-24 12:06:54,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f3af67-423d-4eb1-8e3d-a7e91faf1c0a/GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna.gz --refList GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:12,341] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:12,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:12,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:12,348] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:12,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:12,349] [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
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	100.0	3021	3024	95	conclusive
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	99.9901	3000	3024	95	conclusive
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	91.4431	2411	3024	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	86.5088	2063	3024	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	86.3585	2080	3024	95	below_threshold
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	86.121	2179	3024	95	below_threshold
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	86.1074	2137	3024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,350] [INFO] DFAST Taxonomy check result was written to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:07:12,351] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:12,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:12,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/checkm_data
[2024-01-24 12:07:12,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:12,429] [INFO] Task started: CheckM
[2024-01-24 12:07:12,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/checkm_input GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:08:28,817] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:28,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:28,844] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:28,845] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:28,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:08:28,845] [INFO] Task started: Blastn
[2024-01-24 12:08:28,845] [INFO] Running command: blastn -query GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg85a95df4-bbfa-454e-961d-f13bc8ff0df3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:30,684] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:30,687] [INFO] Selected 8 target genomes.
[2024-01-24 12:08:30,687] [INFO] Target genome list was writen to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:30,693] [INFO] Task started: fastANI
[2024-01-24 12:08:30,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg80f3af67-423d-4eb1-8e3d-a7e91faf1c0a/GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna.gz --refList GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:51,174] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:51,182] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:51,183] [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_900107455.1	s__Asanoa ishikariensis	100.0	3021	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900188485.1	s__Asanoa hainanensis	91.4369	2412	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862515.1	s__Asanoa iriomotensis	86.4877	2067	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862555.1	s__Asanoa siamensis	86.3453	2083	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387075.1	s__Asanoa ferruginea	86.1259	2179	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018324255.1	s__Polymorphospora rubra	79.5021	1173	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Polymorphospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011764425.1	s__Phytohabitans houttuyneae	79.0245	1385	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285795.1	s__KBS50 sp002285795	78.9505	1046	3024	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__KBS50	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:51,184] [INFO] GTDB search result was written to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:51,185] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:51,188] [INFO] DFAST_QC result json was written to GCF_900107455.1_IMG-taxon_2690315652_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:08:51,188] [INFO] DFAST_QC completed!
[2024-01-24 12:08:51,188] [INFO] Total running time: 0h2m27s