[2024-01-25 18:25:06,043] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:06,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:06,046] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference
[2024-01-25 18:25:07,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:07,206] [INFO] Task started: Prodigal
[2024-01-25 18:25:07,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgbabd704b-aac7-405c-99a2-8400918affe5/GCF_028401405.1_ASM2840140v1_genomic.fna.gz | prodigal -d GCF_028401405.1_ASM2840140v1_genomic.fna/cds.fna -a GCF_028401405.1_ASM2840140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:31,501] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:31,502] [INFO] Task started: HMMsearch
[2024-01-25 18:25:31,502] [INFO] Running command: hmmsearch --tblout GCF_028401405.1_ASM2840140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/reference_markers.hmm GCF_028401405.1_ASM2840140v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:31,828] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:31,829] [INFO] Found 6/6 markers.
[2024-01-25 18:25:31,892] [INFO] Query marker FASTA was written to GCF_028401405.1_ASM2840140v1_genomic.fna/markers.fasta
[2024-01-25 18:25:31,893] [INFO] Task started: Blastn
[2024-01-25 18:25:31,893] [INFO] Running command: blastn -query GCF_028401405.1_ASM2840140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/reference_markers.fasta -out GCF_028401405.1_ASM2840140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:33,128] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:33,130] [INFO] Selected 14 target genomes.
[2024-01-25 18:25:33,131] [INFO] Target genome list was writen to GCF_028401405.1_ASM2840140v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:33,137] [INFO] Task started: fastANI
[2024-01-25 18:25:33,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgbabd704b-aac7-405c-99a2-8400918affe5/GCF_028401405.1_ASM2840140v1_genomic.fna.gz --refList GCF_028401405.1_ASM2840140v1_genomic.fna/target_genomes.txt --output GCF_028401405.1_ASM2840140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:26:06,814] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:06,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:26:06,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:26:06,828] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:26:06,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:26:06,829] [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
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	93.4147	1812	2873	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	93.3823	2212	2873	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	93.0172	1837	2873	95	below_threshold
Streptomyces neyagawaensis	strain=NRRL B-3092	GCA_001418645.1	42238	42238	type	True	92.8177	1629	2873	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	87.6844	2071	2873	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	87.5742	2076	2873	95	below_threshold
Streptomyces phaeolivaceus	strain=GY16	GCA_009184865.1	2653200	2653200	type	True	87.5341	2006	2873	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	87.4537	2034	2873	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	87.3918	1957	2873	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	87.2742	2044	2873	95	below_threshold
Streptomyces spinoverrucosus	strain=JCM 5077	GCA_014651195.1	284043	284043	type	True	84.2241	1720	2873	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.0008	1618	2873	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	83.8357	1861	2873	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	83.54	1590	2873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:26:06,830] [INFO] DFAST Taxonomy check result was written to GCF_028401405.1_ASM2840140v1_genomic.fna/tc_result.tsv
[2024-01-25 18:26:06,831] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:26:06,832] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:26:06,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/checkm_data
[2024-01-25 18:26:06,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:26:06,913] [INFO] Task started: CheckM
[2024-01-25 18:26:06,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028401405.1_ASM2840140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028401405.1_ASM2840140v1_genomic.fna/checkm_input GCF_028401405.1_ASM2840140v1_genomic.fna/checkm_result
[2024-01-25 18:28:25,508] [INFO] Task succeeded: CheckM
[2024-01-25 18:28:25,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 18:28:25,534] [INFO] ===== Completeness check finished =====
[2024-01-25 18:28:25,534] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:28:25,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028401405.1_ASM2840140v1_genomic.fna/markers.fasta)
[2024-01-25 18:28:25,535] [INFO] Task started: Blastn
[2024-01-25 18:28:25,535] [INFO] Running command: blastn -query GCF_028401405.1_ASM2840140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd7bfb44-40c5-439a-9561-095fa3dad24d/dqc_reference/reference_markers_gtdb.fasta -out GCF_028401405.1_ASM2840140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:27,664] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:27,668] [INFO] Selected 10 target genomes.
[2024-01-25 18:28:27,668] [INFO] Target genome list was writen to GCF_028401405.1_ASM2840140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:28:27,674] [INFO] Task started: fastANI
[2024-01-25 18:28:27,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgbabd704b-aac7-405c-99a2-8400918affe5/GCF_028401405.1_ASM2840140v1_genomic.fna.gz --refList GCF_028401405.1_ASM2840140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028401405.1_ASM2840140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:28:52,157] [INFO] Task succeeded: fastANI
[2024-01-25 18:28:52,164] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:28:52,165] [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_009857135.1	s__Streptomyces sp009857135	98.6106	2308	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900290235.1	s__Streptomyces sp900290235	93.4212	2243	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	96.28	96.28	0.86	0.86	2	-
GCF_001419765.1	s__Streptomyces torulosus	93.3885	1814	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6665	N/A	N/A	N/A	N/A	1	-
GCF_001418475.1	s__Streptomyces ossamyceticus	93.0158	1837	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6547	98.97	98.97	0.90	0.90	2	-
GCF_001418645.1	s__Streptomyces neyagawaensis	92.8103	1629	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.4249	N/A	N/A	N/A	N/A	1	-
GCF_900114955.1	s__Streptomyces sp900114955	87.6365	2054	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.68	97.04	0.90	0.85	10	-
GCF_009184865.1	s__Streptomyces phaeolivaceus	87.5393	2005	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383595.1	s__Streptomyces bottropensis	87.4866	2028	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.7549	99.99	99.99	1.00	1.00	3	-
GCF_014203845.1	s__Streptomyces scabiei_E	87.3557	2032	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.80	0.80	2	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.2029	1831	2873	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:28:52,167] [INFO] GTDB search result was written to GCF_028401405.1_ASM2840140v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:28:52,167] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:28:52,170] [INFO] DFAST_QC result json was written to GCF_028401405.1_ASM2840140v1_genomic.fna/dqc_result.json
[2024-01-25 18:28:52,171] [INFO] DFAST_QC completed!
[2024-01-25 18:28:52,171] [INFO] Total running time: 0h3m46s