[2024-01-24 12:31:51,282] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:51,284] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:51,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference
[2024-01-24 12:31:52,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:52,538] [INFO] Task started: Prodigal
[2024-01-24 12:31:52,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a142960-a2eb-465b-90b3-9212a81e288d/GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/cds.fna -a GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:13,273] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:13,273] [INFO] Task started: HMMsearch
[2024-01-24 12:32:13,273] [INFO] Running command: hmmsearch --tblout GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/reference_markers.hmm GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:13,578] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:13,580] [INFO] Found 6/6 markers.
[2024-01-24 12:32:13,636] [INFO] Query marker FASTA was written to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:13,637] [INFO] Task started: Blastn
[2024-01-24 12:32:13,637] [INFO] Running command: blastn -query GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/reference_markers.fasta -out GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:15,045] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:15,049] [INFO] Selected 9 target genomes.
[2024-01-24 12:32:15,049] [INFO] Target genome list was writen to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:15,052] [INFO] Task started: fastANI
[2024-01-24 12:32:15,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a142960-a2eb-465b-90b3-9212a81e288d/GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna.gz --refList GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:30,578] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:30,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:30,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:30,587] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:30,587] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:30,588] [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
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	100.0	2085	2085	95	conclusive
Saccharopolyspora endophytica	strain=KCTC 19397	GCA_018070075.1	543886	543886	type	True	89.3964	1682	2085	95	below_threshold
Saccharopolyspora terrae	strain=16K309	GCA_004348435.1	2530384	2530384	type	True	89.351	1609	2085	95	below_threshold
Saccharopolyspora karakumensis	strain=5K548	GCA_004349225.1	2530386	2530386	type	True	89.3462	1573	2085	95	below_threshold
Saccharopolyspora rhizosphaerae	strain=H219	GCA_003931915.1	2492662	2492662	type	True	88.5773	1538	2085	95	below_threshold
Saccharopolyspora aridisoli	strain=16K404	GCA_004348445.1	2530385	2530385	type	True	88.506	1604	2085	95	below_threshold
Saccharopolyspora dendranthemae	strain=DSM 46699	GCA_007829955.1	1181886	1181886	type	True	87.9881	1703	2085	95	below_threshold
Halopolyspora algeriensis	strain=CECT 8575	GCA_003337235.1	1500506	1500506	type	True	79.2669	703	2085	95	below_threshold
Halopolyspora algeriensis	strain=DSM 46680	GCA_006716575.1	1500506	1500506	type	True	79.2093	696	2085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:30,589] [INFO] DFAST Taxonomy check result was written to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:30,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:30,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:30,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/checkm_data
[2024-01-24 12:32:30,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:30,653] [INFO] Task started: CheckM
[2024-01-24 12:32:30,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/checkm_input GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:44,844] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:44,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:44,870] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:44,870] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:44,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:44,871] [INFO] Task started: Blastn
[2024-01-24 12:33:44,871] [INFO] Running command: blastn -query GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg01688f42-438c-47ba-a7c2-f34d012bcc99/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:46,838] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:46,844] [INFO] Selected 7 target genomes.
[2024-01-24 12:33:46,844] [INFO] Target genome list was writen to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:47,410] [INFO] Task started: fastANI
[2024-01-24 12:33:47,411] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a142960-a2eb-465b-90b3-9212a81e288d/GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna.gz --refList GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:59,909] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:59,925] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:59,926] [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_900116135.1	s__Saccharopolyspora flava	100.0	2085	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018070075.1	s__Saccharopolyspora endophytica	89.3828	1683	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	96.33	95.95	0.87	0.87	3	-
GCF_003931915.1	s__Saccharopolyspora rhizosphaerae	88.5566	1540	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348445.1	s__Saccharopolyspora sp004348445	88.5491	1600	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829955.1	s__Saccharopolyspora dendranthemae	87.9813	1704	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014137975.1	s__Halosaccharopolyspora lacisalsi	79.4889	793	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halosaccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337235.1	s__Halopolyspora algeriensis	79.2599	704	2085	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Halopolyspora	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:59,929] [INFO] GTDB search result was written to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:59,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:59,935] [INFO] DFAST_QC result json was written to GCF_900116135.1_IMG-taxon_2599185150_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:33:59,935] [INFO] DFAST_QC completed!
[2024-01-24 12:33:59,936] [INFO] Total running time: 0h2m9s