[2024-01-24 13:17:47,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:47,464] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:47,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference
[2024-01-24 13:17:48,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:48,832] [INFO] Task started: Prodigal
[2024-01-24 13:17:48,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg48483116-b2c9-434c-8727-409406468c81/GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/cds.fna -a GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:17,148] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:17,149] [INFO] Task started: HMMsearch
[2024-01-24 13:18:17,149] [INFO] Running command: hmmsearch --tblout GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/reference_markers.hmm GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:17,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:17,658] [INFO] Found 6/6 markers.
[2024-01-24 13:18:17,738] [INFO] Query marker FASTA was written to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:18:17,739] [INFO] Task started: Blastn
[2024-01-24 13:18:17,739] [INFO] Running command: blastn -query GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/reference_markers.fasta -out GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:19,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:19,132] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:19,132] [INFO] Target genome list was writen to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:18:19,137] [INFO] Task started: fastANI
[2024-01-24 13:18:19,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg48483116-b2c9-434c-8727-409406468c81/GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna.gz --refList GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:52,837] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,837] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:52,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:52,850] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:52,850] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:52,850] [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
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	100.0	3160	3177	95	conclusive
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	84.3928	1795	3177	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	83.3511	1681	3177	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.2818	1767	3177	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	83.2075	1371	3177	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	83.1654	1666	3177	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	83.0942	1606	3177	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	83.0061	1635	3177	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	82.8658	1754	3177	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	82.7808	1627	3177	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.6792	1214	3177	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.9131	1307	3177	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.7833	1179	3177	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	79.6744	1107	3177	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	79.1647	1271	3177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,852] [INFO] DFAST Taxonomy check result was written to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:18:52,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:52,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:52,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/checkm_data
[2024-01-24 13:18:52,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:52,938] [INFO] Task started: CheckM
[2024-01-24 13:18:52,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/checkm_input GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:21:23,920] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:23,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:23,948] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:23,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:23,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:21:23,949] [INFO] Task started: Blastn
[2024-01-24 13:21:23,949] [INFO] Running command: blastn -query GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b131090-96ab-4759-9466-c6a1d4c23ac1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:26,110] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:26,114] [INFO] Selected 11 target genomes.
[2024-01-24 13:21:26,114] [INFO] Target genome list was writen to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:26,140] [INFO] Task started: fastANI
[2024-01-24 13:21:26,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg48483116-b2c9-434c-8727-409406468c81/GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna.gz --refList GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:21:51,826] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:51,846] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:21:51,847] [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_900107965.1	s__Streptomyces yanglinensis	100.0	3163	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016756395.1	s__Streptomyces sp016756395	87.1902	1932	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103985.1	s__Streptomyces guanduensis	84.4008	1794	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091855.1	s__Streptomyces sp900091855	83.3542	1438	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110255.1	s__Streptomyces rubidus	83.2346	1776	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112845.1	s__Streptomyces alni	83.1266	1675	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783685.1	s__Streptomyces sp009783685	83.1163	1105	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	83.072	1610	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900142575.1	s__Streptomyces paucisporeus	82.9987	1637	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918855.1	s__Streptomyces acididurans	82.8207	1763	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	82.7273	1569	3177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:21:51,849] [INFO] GTDB search result was written to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:21:51,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:21:51,854] [INFO] DFAST_QC result json was written to GCF_900107965.1_IMG-taxon_2667527441_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:21:51,854] [INFO] DFAST_QC completed!
[2024-01-24 13:21:51,854] [INFO] Total running time: 0h4m4s