[2023-06-29 20:10:46,208] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:10:46,212] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:10:46,212] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference
[2023-06-29 20:10:47,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:10:47,682] [INFO] Task started: Prodigal
[2023-06-29 20:10:47,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a88b2b2-c7ca-46e1-ba47-5fd89ada4a1f/GCA_016780965.1_ASM1678096v1_genomic.fna.gz | prodigal -d GCA_016780965.1_ASM1678096v1_genomic.fna/cds.fna -a GCA_016780965.1_ASM1678096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:10:53,295] [INFO] Task succeeded: Prodigal
[2023-06-29 20:10:53,295] [INFO] Task started: HMMsearch
[2023-06-29 20:10:53,295] [INFO] Running command: hmmsearch --tblout GCA_016780965.1_ASM1678096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/reference_markers.hmm GCA_016780965.1_ASM1678096v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:10:53,573] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:10:53,575] [INFO] Found 6/6 markers.
[2023-06-29 20:10:53,607] [INFO] Query marker FASTA was written to GCA_016780965.1_ASM1678096v1_genomic.fna/markers.fasta
[2023-06-29 20:10:53,607] [INFO] Task started: Blastn
[2023-06-29 20:10:53,607] [INFO] Running command: blastn -query GCA_016780965.1_ASM1678096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/reference_markers.fasta -out GCA_016780965.1_ASM1678096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:10:54,440] [INFO] Task succeeded: Blastn
[2023-06-29 20:10:54,444] [INFO] Selected 32 target genomes.
[2023-06-29 20:10:54,444] [INFO] Target genome list was writen to GCA_016780965.1_ASM1678096v1_genomic.fna/target_genomes.txt
[2023-06-29 20:10:54,455] [INFO] Task started: fastANI
[2023-06-29 20:10:54,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a88b2b2-c7ca-46e1-ba47-5fd89ada4a1f/GCA_016780965.1_ASM1678096v1_genomic.fna.gz --refList GCA_016780965.1_ASM1678096v1_genomic.fna/target_genomes.txt --output GCA_016780965.1_ASM1678096v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:11:24,243] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:24,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:11:24,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:11:24,263] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:11:24,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:11:24,263] [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
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	77.0991	51	574	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	76.3187	55	574	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	76.3182	55	574	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	76.0776	53	574	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	76.0377	65	574	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	75.8438	51	574	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	75.8189	57	574	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	75.7963	52	574	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_005869865.1	2382123	2382123	type	True	75.7963	52	574	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	75.759	59	574	95	below_threshold
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	75.6854	57	574	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:11:24,265] [INFO] DFAST Taxonomy check result was written to GCA_016780965.1_ASM1678096v1_genomic.fna/tc_result.tsv
[2023-06-29 20:11:24,266] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:11:24,266] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:11:24,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/checkm_data
[2023-06-29 20:11:24,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:11:24,288] [INFO] Task started: CheckM
[2023-06-29 20:11:24,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016780965.1_ASM1678096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016780965.1_ASM1678096v1_genomic.fna/checkm_input GCA_016780965.1_ASM1678096v1_genomic.fna/checkm_result
[2023-06-29 20:11:47,326] [INFO] Task succeeded: CheckM
[2023-06-29 20:11:47,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:11:47,348] [INFO] ===== Completeness check finished =====
[2023-06-29 20:11:47,348] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:11:47,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016780965.1_ASM1678096v1_genomic.fna/markers.fasta)
[2023-06-29 20:11:47,349] [INFO] Task started: Blastn
[2023-06-29 20:11:47,349] [INFO] Running command: blastn -query GCA_016780965.1_ASM1678096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd365414-90b0-4f73-9f66-dcd0e61eff37/dqc_reference/reference_markers_gtdb.fasta -out GCA_016780965.1_ASM1678096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:11:48,420] [INFO] Task succeeded: Blastn
[2023-06-29 20:11:48,425] [INFO] Selected 12 target genomes.
[2023-06-29 20:11:48,425] [INFO] Target genome list was writen to GCA_016780965.1_ASM1678096v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:11:48,433] [INFO] Task started: fastANI
[2023-06-29 20:11:48,433] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a88b2b2-c7ca-46e1-ba47-5fd89ada4a1f/GCA_016780965.1_ASM1678096v1_genomic.fna.gz --refList GCA_016780965.1_ASM1678096v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016780965.1_ASM1678096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:11:53,804] [INFO] Task succeeded: fastANI
[2023-06-29 20:11:53,819] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:11:53,819] [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
GCA_002729215.1	s__S36-B12 sp002729215	97.3672	464	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.32	97.43	0.87	0.81	12	conclusive
GCA_012103605.1	s__S36-B12 sp012103605	91.0358	423	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	95.57	95.57	0.76	0.76	2	-
GCA_010029945.1	s__S36-B12 sp010029945	90.7711	368	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	98.25	98.18	0.79	0.75	5	-
GCA_002728915.1	s__S36-B12 sp002728915	90.7648	440	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	99.13	98.99	0.85	0.80	4	-
GCA_002694095.1	s__S36-B12 sp002694095	89.7945	427	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	97.65	97.49	0.82	0.80	3	-
GCA_018402235.1	s__S36-B12 sp018402235	77.6653	156	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__S36-B12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699015.1	s__WLND01 sp009699015	76.2066	67	574	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-29 20:11:53,821] [INFO] GTDB search result was written to GCA_016780965.1_ASM1678096v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:11:53,822] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:11:53,825] [INFO] DFAST_QC result json was written to GCA_016780965.1_ASM1678096v1_genomic.fna/dqc_result.json
[2023-06-29 20:11:53,825] [INFO] DFAST_QC completed!
[2023-06-29 20:11:53,826] [INFO] Total running time: 0h1m8s