[2024-01-24 14:14:45,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference
[2024-01-24 14:14:46,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,949] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg3da37dd7-be91-4caf-aeef-9840c6012dbb/GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/cds.fna -a GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:14,584] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:14,585] [INFO] Task started: HMMsearch
[2024-01-24 14:15:14,585] [INFO] Running command: hmmsearch --tblout GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/reference_markers.hmm GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:15,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:15,018] [INFO] Found 6/6 markers.
[2024-01-24 14:15:15,097] [INFO] Query marker FASTA was written to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:15:15,097] [INFO] Task started: Blastn
[2024-01-24 14:15:15,097] [INFO] Running command: blastn -query GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/reference_markers.fasta -out GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:16,422] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:16,425] [INFO] Selected 15 target genomes.
[2024-01-24 14:15:16,425] [INFO] Target genome list was writen to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:15:16,434] [INFO] Task started: fastANI
[2024-01-24 14:15:16,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da37dd7-be91-4caf-aeef-9840c6012dbb/GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna.gz --refList GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:56,204] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:56,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:56,205] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:56,217] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:56,217] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:56,217] [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
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	100.0	3393	3394	95	conclusive
Actinomadura darangshiensis	strain=DSM 45941	GCA_004349235.1	705336	705336	type	True	88.4259	2103	3394	95	below_threshold
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	87.6879	2158	3394	95	below_threshold
Actinomadura citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	87.6414	2147	3394	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	87.6346	2016	3394	95	below_threshold
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	87.6095	2079	3394	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	87.6076	2049	3394	95	below_threshold
Actinomadura bangladeshensis	strain=DSM 45347	GCA_004348335.1	453573	453573	type	True	87.1398	1849	3394	95	below_threshold
Actinomadura meyerae	strain=DSM 44715	GCA_900188445.1	240840	240840	type	True	86.9839	2067	3394	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	86.8539	1813	3394	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.5986	2063	3394	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.5413	1657	3394	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8437	1718	3394	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.5139	1571	3394	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.0073	1573	3394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:56,219] [INFO] DFAST Taxonomy check result was written to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:56,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:56,220] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:56,220] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/checkm_data
[2024-01-24 14:15:56,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:56,316] [INFO] Task started: CheckM
[2024-01-24 14:15:56,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/checkm_input GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:17:28,267] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:28,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 14:17:28,294] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:28,294] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:28,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:17:28,295] [INFO] Task started: Blastn
[2024-01-24 14:17:28,295] [INFO] Running command: blastn -query GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg44d69fa0-047d-445a-bfe0-3dc409c7fc7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:30,425] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:30,429] [INFO] Selected 11 target genomes.
[2024-01-24 14:17:30,429] [INFO] Target genome list was writen to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:30,454] [INFO] Task started: fastANI
[2024-01-24 14:17:30,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg3da37dd7-be91-4caf-aeef-9840c6012dbb/GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna.gz --refList GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:18:00,547] [INFO] Task succeeded: fastANI
[2024-01-24 14:18:00,563] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:18:00,563] [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_900115095.1	s__Spirillospora madurae	100.0	3393	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	conclusive
GCF_004349235.1	s__Spirillospora darangshiensis	88.4229	2105	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008327685.1	s__Spirillospora sp008327685	87.6813	2210	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409045.1	s__Spirillospora citrea	87.6576	2163	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014208105.1	s__Spirillospora coerulea	87.644	2043	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900188105.1	s__Spirillospora mexicana	87.6343	2075	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409365.1	s__Spirillospora luteofluorescens	87.4767	2172	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006547145.1	s__Spirillospora sp006547145	87.3354	2136	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013364275.1	s__Spirillospora sp013364275	86.9748	2149	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188445.1	s__Spirillospora meyerae	86.9721	2069	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889745.1	s__Spirillospora geliboluensis	86.7871	1822	3394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:18:00,565] [INFO] GTDB search result was written to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:18:00,566] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:18:00,576] [INFO] DFAST_QC result json was written to GCF_900115095.1_IMG-taxon_2634166331_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:18:00,577] [INFO] DFAST_QC completed!
[2024-01-24 14:18:00,577] [INFO] Total running time: 0h3m15s