[2024-01-24 13:32:17,168] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:17,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:17,174] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference
[2024-01-24 13:32:18,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:18,585] [INFO] Task started: Prodigal
[2024-01-24 13:32:18,585] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa7a3cc0-3837-44cc-8bac-9bb1df4754b6/GCF_004323735.1_ASM432373v1_genomic.fna.gz | prodigal -d GCF_004323735.1_ASM432373v1_genomic.fna/cds.fna -a GCF_004323735.1_ASM432373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:36,434] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:36,434] [INFO] Task started: HMMsearch
[2024-01-24 13:32:36,434] [INFO] Running command: hmmsearch --tblout GCF_004323735.1_ASM432373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/reference_markers.hmm GCF_004323735.1_ASM432373v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:36,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:36,776] [INFO] Found 6/6 markers.
[2024-01-24 13:32:36,827] [INFO] Query marker FASTA was written to GCF_004323735.1_ASM432373v1_genomic.fna/markers.fasta
[2024-01-24 13:32:36,828] [INFO] Task started: Blastn
[2024-01-24 13:32:36,828] [INFO] Running command: blastn -query GCF_004323735.1_ASM432373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/reference_markers.fasta -out GCF_004323735.1_ASM432373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:38,064] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:38,067] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:38,068] [INFO] Target genome list was writen to GCF_004323735.1_ASM432373v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:38,078] [INFO] Task started: fastANI
[2024-01-24 13:32:38,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7a3cc0-3837-44cc-8bac-9bb1df4754b6/GCF_004323735.1_ASM432373v1_genomic.fna.gz --refList GCF_004323735.1_ASM432373v1_genomic.fna/target_genomes.txt --output GCF_004323735.1_ASM432373v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:03,152] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:03,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:03,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:03,167] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:03,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:03,167] [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
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	100.0	1937	1937	95	conclusive
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	85.324	1385	1937	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	84.7037	1326	1937	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.8922	911	1937	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	80.6962	899	1937	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	80.6875	825	1937	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	80.5191	949	1937	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.29	1041	1937	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	79.9603	717	1937	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	79.9357	771	1937	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.8438	757	1937	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	79.8374	834	1937	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.2965	782	1937	95	below_threshold
Nocardiopsis lucentensis	strain=DSM 44048	GCA_000341125.1	53441	53441	type	True	79.2916	625	1937	95	below_threshold
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	79.0781	799	1937	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	78.872	629	1937	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	78.393	562	1937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:03,169] [INFO] DFAST Taxonomy check result was written to GCF_004323735.1_ASM432373v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:03,169] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:03,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:03,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/checkm_data
[2024-01-24 13:33:03,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:03,228] [INFO] Task started: CheckM
[2024-01-24 13:33:03,228] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004323735.1_ASM432373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004323735.1_ASM432373v1_genomic.fna/checkm_input GCF_004323735.1_ASM432373v1_genomic.fna/checkm_result
[2024-01-24 13:34:03,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:03,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,391] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:03,392] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:03,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004323735.1_ASM432373v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:03,392] [INFO] Task started: Blastn
[2024-01-24 13:34:03,393] [INFO] Running command: blastn -query GCF_004323735.1_ASM432373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2d2cfe1-cef8-4072-969a-e1614cbdb87c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004323735.1_ASM432373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:05,175] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:05,179] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:05,180] [INFO] Target genome list was writen to GCF_004323735.1_ASM432373v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:05,203] [INFO] Task started: fastANI
[2024-01-24 13:34:05,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa7a3cc0-3837-44cc-8bac-9bb1df4754b6/GCF_004323735.1_ASM432373v1_genomic.fna.gz --refList GCF_004323735.1_ASM432373v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004323735.1_ASM432373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:21,306] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:21,320] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:21,320] [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_004323735.1	s__Streptomonospora sp004323735	100.0	1936	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009728995.1	s__Streptomonospora sp009728995	86.0134	1430	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826685.1	s__Streptomonospora alba	85.297	1389	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204715.1	s__Streptomonospora salina	84.7185	1320	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	83.254	1280	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	81.3799	1020	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	80.8139	916	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	80.2881	1043	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341125.1	s__Nocardiopsis lucentensis	79.2613	629	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341005.1	s__Nocardiopsis alkaliphila	78.366	566	1937	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:21,322] [INFO] GTDB search result was written to GCF_004323735.1_ASM432373v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:21,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:21,326] [INFO] DFAST_QC result json was written to GCF_004323735.1_ASM432373v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:21,326] [INFO] DFAST_QC completed!
[2024-01-24 13:34:21,326] [INFO] Total running time: 0h2m4s