[2024-01-24 13:46:01,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference
[2024-01-24 13:46:02,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,479] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,479] [INFO] Running command: gunzip -c /var/lib/cwl/stgac512b79-b8cb-4717-8bd6-a6f0c5f98e45/GCF_020859565.1_ASM2085956v1_genomic.fna.gz | prodigal -d GCF_020859565.1_ASM2085956v1_genomic.fna/cds.fna -a GCF_020859565.1_ASM2085956v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:36,234] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:36,235] [INFO] Task started: HMMsearch
[2024-01-24 13:46:36,235] [INFO] Running command: hmmsearch --tblout GCF_020859565.1_ASM2085956v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/reference_markers.hmm GCF_020859565.1_ASM2085956v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:36,675] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:36,677] [INFO] Found 6/6 markers.
[2024-01-24 13:46:36,759] [INFO] Query marker FASTA was written to GCF_020859565.1_ASM2085956v1_genomic.fna/markers.fasta
[2024-01-24 13:46:36,759] [INFO] Task started: Blastn
[2024-01-24 13:46:36,760] [INFO] Running command: blastn -query GCF_020859565.1_ASM2085956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/reference_markers.fasta -out GCF_020859565.1_ASM2085956v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:38,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:38,126] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:38,127] [INFO] Target genome list was writen to GCF_020859565.1_ASM2085956v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:38,200] [INFO] Task started: fastANI
[2024-01-24 13:46:38,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgac512b79-b8cb-4717-8bd6-a6f0c5f98e45/GCF_020859565.1_ASM2085956v1_genomic.fna.gz --refList GCF_020859565.1_ASM2085956v1_genomic.fna/target_genomes.txt --output GCF_020859565.1_ASM2085956v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:19,323] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:19,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:19,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:19,339] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:47:19,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:47:19,340] [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 texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	91.928	2382	3407	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	90.7537	2306	3407	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	90.2467	2283	3407	95	below_threshold
Saccharothrix deserti	strain=BMP B8144	GCA_009769385.1	2593674	2593674	type	True	88.1106	2209	3407	95	below_threshold
Saccharothrix ecbatanensis	strain=DSM 45486	GCA_014205015.1	1105145	1105145	type	True	87.5448	2119	3407	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	84.8454	2105	3407	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	84.796	2068	3407	95	below_threshold
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	83.7234	1677	3407	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	83.5135	1527	3407	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	83.3775	1674	3407	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	83.2832	1789	3407	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	82.8012	1574	3407	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.2971	1442	3407	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	80.0775	1418	3407	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.0174	958	3407	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9152	1227	3407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,341] [INFO] DFAST Taxonomy check result was written to GCF_020859565.1_ASM2085956v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:19,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:19,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:19,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/checkm_data
[2024-01-24 13:47:19,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:19,435] [INFO] Task started: CheckM
[2024-01-24 13:47:19,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020859565.1_ASM2085956v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020859565.1_ASM2085956v1_genomic.fna/checkm_input GCF_020859565.1_ASM2085956v1_genomic.fna/checkm_result
[2024-01-24 13:49:48,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:48,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 16.67%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:48,860] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:48,860] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:48,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020859565.1_ASM2085956v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:48,861] [INFO] Task started: Blastn
[2024-01-24 13:49:48,861] [INFO] Running command: blastn -query GCF_020859565.1_ASM2085956v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f363517-5a9d-4d58-af0f-9ce604f21426/dqc_reference/reference_markers_gtdb.fasta -out GCF_020859565.1_ASM2085956v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,029] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:51,029] [INFO] Target genome list was writen to GCF_020859565.1_ASM2085956v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,104] [INFO] Task started: fastANI
[2024-01-24 13:49:51,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgac512b79-b8cb-4717-8bd6-a6f0c5f98e45/GCF_020859565.1_ASM2085956v1_genomic.fna.gz --refList GCF_020859565.1_ASM2085956v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020859565.1_ASM2085956v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:28,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:28,101] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:28,101] [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_001280085.1	s__Actinosynnema sp001280085	92.3311	2530	3407	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	91.9519	2378	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_003014735.1	s__Actinosynnema carneum	90.721	2311	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_006716745.1	s__Actinosynnema saharense	90.2087	2291	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	88.1401	2201	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984175.1	s__Actinosynnema sp001984175	87.9165	2105	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716595.1	s__Actinosynnema sp000716595	87.7641	2067	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205015.1	s__Actinosynnema ecbatanense	87.5519	2118	3407	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	84.8328	2107	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014203665.1	s__Actinosynnema tamanrassetense	83.6947	1682	3407	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	83.484	1532	3407	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	83.3788	1674	3407	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328705.1	s__Actinosynnema espanaense	83.3009	1786	3407	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 13:50:28,103] [INFO] GTDB search result was written to GCF_020859565.1_ASM2085956v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:28,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:28,107] [INFO] DFAST_QC result json was written to GCF_020859565.1_ASM2085956v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:28,107] [INFO] DFAST_QC completed!
[2024-01-24 13:50:28,107] [INFO] Total running time: 0h4m27s