[2024-01-24 13:49:44,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:44,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:44,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference
[2024-01-24 13:49:45,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:45,969] [INFO] Task started: Prodigal
[2024-01-24 13:49:45,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgad70a90c-8118-49ce-b1aa-e60fdc719c06/GCF_019375475.1_ASM1937547v1_genomic.fna.gz | prodigal -d GCF_019375475.1_ASM1937547v1_genomic.fna/cds.fna -a GCF_019375475.1_ASM1937547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:14,514] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:14,515] [INFO] Task started: HMMsearch
[2024-01-24 13:50:14,515] [INFO] Running command: hmmsearch --tblout GCF_019375475.1_ASM1937547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/reference_markers.hmm GCF_019375475.1_ASM1937547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:14,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:14,898] [INFO] Found 6/6 markers.
[2024-01-24 13:50:14,958] [INFO] Query marker FASTA was written to GCF_019375475.1_ASM1937547v1_genomic.fna/markers.fasta
[2024-01-24 13:50:14,959] [INFO] Task started: Blastn
[2024-01-24 13:50:14,959] [INFO] Running command: blastn -query GCF_019375475.1_ASM1937547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/reference_markers.fasta -out GCF_019375475.1_ASM1937547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:16,350] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:16,355] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:16,356] [INFO] Target genome list was writen to GCF_019375475.1_ASM1937547v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:16,362] [INFO] Task started: fastANI
[2024-01-24 13:50:16,362] [INFO] Running command: fastANI --query /var/lib/cwl/stgad70a90c-8118-49ce-b1aa-e60fdc719c06/GCF_019375475.1_ASM1937547v1_genomic.fna.gz --refList GCF_019375475.1_ASM1937547v1_genomic.fna/target_genomes.txt --output GCF_019375475.1_ASM1937547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:46,994] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:46,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:46,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:47,006] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:47,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:47,007] [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
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	100.0	2655	2658	95	conclusive
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	85.2244	1828	2658	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	85.0999	1737	2658	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	85.0203	1635	2658	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	84.9272	1709	2658	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	83.7965	1585	2658	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	83.1723	1573	2658	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	82.7492	1638	2658	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	82.7022	1664	2658	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	82.0469	1375	2658	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.5516	996	2658	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.3228	927	2658	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.7194	811	2658	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.5678	1093	2658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,009] [INFO] DFAST Taxonomy check result was written to GCF_019375475.1_ASM1937547v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:47,009] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:47,009] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:47,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/checkm_data
[2024-01-24 13:50:47,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:47,087] [INFO] Task started: CheckM
[2024-01-24 13:50:47,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019375475.1_ASM1937547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019375475.1_ASM1937547v1_genomic.fna/checkm_input GCF_019375475.1_ASM1937547v1_genomic.fna/checkm_result
[2024-01-24 13:52:53,661] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:53,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:53,691] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:53,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:53,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019375475.1_ASM1937547v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:53,693] [INFO] Task started: Blastn
[2024-01-24 13:52:53,693] [INFO] Running command: blastn -query GCF_019375475.1_ASM1937547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a350e8-6245-422e-a98b-311d3bf3805f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019375475.1_ASM1937547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:55,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:55,851] [INFO] Selected 11 target genomes.
[2024-01-24 13:52:55,851] [INFO] Target genome list was writen to GCF_019375475.1_ASM1937547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:55,867] [INFO] Task started: fastANI
[2024-01-24 13:52:55,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgad70a90c-8118-49ce-b1aa-e60fdc719c06/GCF_019375475.1_ASM1937547v1_genomic.fna.gz --refList GCF_019375475.1_ASM1937547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019375475.1_ASM1937547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:21,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:21,632] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:53:21,632] [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_000328705.1	s__Actinosynnema espanaense	85.2166	1829	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	85.1272	1732	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	84.9911	1638	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	84.9108	1712	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	83.8151	1582	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	83.185	1572	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280085.1	s__Actinosynnema sp001280085	82.9678	1597	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	82.9607	1633	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_000716595.1	s__Actinosynnema sp000716595	82.8891	1464	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	82.6619	1671	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	82.069	1372	2658	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:21,634] [INFO] GTDB search result was written to GCF_019375475.1_ASM1937547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:21,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:21,638] [INFO] DFAST_QC result json was written to GCF_019375475.1_ASM1937547v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:21,638] [INFO] DFAST_QC completed!
[2024-01-24 13:53:21,638] [INFO] Total running time: 0h3m37s