[2024-01-25 20:07:05,438] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:05,440] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:05,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference
[2024-01-25 20:07:06,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:06,576] [INFO] Task started: Prodigal
[2024-01-25 20:07:06,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a5fb519-0aa2-49b3-a11a-aa7adea30e78/GCF_014648455.1_ASM1464845v1_genomic.fna.gz | prodigal -d GCF_014648455.1_ASM1464845v1_genomic.fna/cds.fna -a GCF_014648455.1_ASM1464845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:27,577] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:27,578] [INFO] Task started: HMMsearch
[2024-01-25 20:07:27,578] [INFO] Running command: hmmsearch --tblout GCF_014648455.1_ASM1464845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/reference_markers.hmm GCF_014648455.1_ASM1464845v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:27,899] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:27,900] [INFO] Found 6/6 markers.
[2024-01-25 20:07:27,966] [INFO] Query marker FASTA was written to GCF_014648455.1_ASM1464845v1_genomic.fna/markers.fasta
[2024-01-25 20:07:27,966] [INFO] Task started: Blastn
[2024-01-25 20:07:27,967] [INFO] Running command: blastn -query GCF_014648455.1_ASM1464845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/reference_markers.fasta -out GCF_014648455.1_ASM1464845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:29,217] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:29,226] [INFO] Selected 10 target genomes.
[2024-01-25 20:07:29,226] [INFO] Target genome list was writen to GCF_014648455.1_ASM1464845v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:29,233] [INFO] Task started: fastANI
[2024-01-25 20:07:29,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5fb519-0aa2-49b3-a11a-aa7adea30e78/GCF_014648455.1_ASM1464845v1_genomic.fna.gz --refList GCF_014648455.1_ASM1464845v1_genomic.fna/target_genomes.txt --output GCF_014648455.1_ASM1464845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:55,041] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:55,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:55,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:55,050] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:07:55,050] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:55,050] [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 citrea	strain=JCM 3295	GCA_014648455.1	46158	46158	type	True	100.0	2940	2949	95	conclusive
Actinomadura citrea	strain=DSM 43461	GCA_013409045.1	46158	46158	type	True	99.9971	2947	2949	95	conclusive
Actinomadura mexicana	strain=DSM 44485	GCA_900188105.1	134959	134959	type	True	94.841	2435	2949	95	below_threshold
Actinomadura coerulea	strain=DSM 43675	GCA_014208105.1	46159	46159	type	True	93.6395	2389	2949	95	below_threshold
Actinomadura coerulea	strain=JCM 3320	GCA_014648535.1	46159	46159	type	True	93.6313	2383	2949	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	84.6341	2083	2949	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	84.4092	1597	2949	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	83.8729	1701	2949	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	81.5553	1550	2949	95	below_threshold
Actinomadura rupiterrae	strain=DSM 45251	GCA_024172125.1	559627	559627	type	True	81.2139	1515	2949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:55,051] [INFO] DFAST Taxonomy check result was written to GCF_014648455.1_ASM1464845v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:55,052] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:55,052] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:55,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/checkm_data
[2024-01-25 20:07:55,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:55,131] [INFO] Task started: CheckM
[2024-01-25 20:07:55,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648455.1_ASM1464845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648455.1_ASM1464845v1_genomic.fna/checkm_input GCF_014648455.1_ASM1464845v1_genomic.fna/checkm_result
[2024-01-25 20:09:41,904] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:41,905] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:41,929] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:41,929] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:41,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648455.1_ASM1464845v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:41,930] [INFO] Task started: Blastn
[2024-01-25 20:09:41,931] [INFO] Running command: blastn -query GCF_014648455.1_ASM1464845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357b0738-6187-4020-89e3-c23968a1c79c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648455.1_ASM1464845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:43,916] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:43,919] [INFO] Selected 7 target genomes.
[2024-01-25 20:09:43,919] [INFO] Target genome list was writen to GCF_014648455.1_ASM1464845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:43,958] [INFO] Task started: fastANI
[2024-01-25 20:09:43,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a5fb519-0aa2-49b3-a11a-aa7adea30e78/GCF_014648455.1_ASM1464845v1_genomic.fna.gz --refList GCF_014648455.1_ASM1464845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648455.1_ASM1464845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:10:03,674] [INFO] Task succeeded: fastANI
[2024-01-25 20:10:03,680] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:10:03,680] [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_013409045.1	s__Spirillospora citrea	99.9971	2947	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900188105.1	s__Spirillospora mexicana	94.8576	2433	2949	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	93.677	2553	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208105.1	s__Spirillospora coerulea	93.643	2388	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008327685.1	s__Spirillospora sp008327685	91.8478	2324	2949	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	91.346	2284	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115095.1	s__Spirillospora madurae	87.7631	2109	2949	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	99.34	99.27	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:10:03,682] [INFO] GTDB search result was written to GCF_014648455.1_ASM1464845v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:10:03,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:10:03,684] [INFO] DFAST_QC result json was written to GCF_014648455.1_ASM1464845v1_genomic.fna/dqc_result.json
[2024-01-25 20:10:03,685] [INFO] DFAST_QC completed!
[2024-01-25 20:10:03,685] [INFO] Total running time: 0h2m58s