[2024-01-24 12:22:07,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:07,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:07,452] [INFO] DQC Reference Directory: /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference
[2024-01-24 12:22:08,723] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:08,724] [INFO] Task started: Prodigal
[2024-01-24 12:22:08,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg84cc720c-db6c-4783-af59-78dd75cbe2f8/GCF_006335015.1_ASM633501v1_genomic.fna.gz | prodigal -d GCF_006335015.1_ASM633501v1_genomic.fna/cds.fna -a GCF_006335015.1_ASM633501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:27,016] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:27,016] [INFO] Task started: HMMsearch
[2024-01-24 12:22:27,017] [INFO] Running command: hmmsearch --tblout GCF_006335015.1_ASM633501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/reference_markers.hmm GCF_006335015.1_ASM633501v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:27,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:27,346] [INFO] Found 6/6 markers.
[2024-01-24 12:22:27,413] [INFO] Query marker FASTA was written to GCF_006335015.1_ASM633501v1_genomic.fna/markers.fasta
[2024-01-24 12:22:27,414] [INFO] Task started: Blastn
[2024-01-24 12:22:27,414] [INFO] Running command: blastn -query GCF_006335015.1_ASM633501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/reference_markers.fasta -out GCF_006335015.1_ASM633501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:28,749] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:28,753] [INFO] Selected 13 target genomes.
[2024-01-24 12:22:28,754] [INFO] Target genome list was writen to GCF_006335015.1_ASM633501v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:28,761] [INFO] Task started: fastANI
[2024-01-24 12:22:28,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg84cc720c-db6c-4783-af59-78dd75cbe2f8/GCF_006335015.1_ASM633501v1_genomic.fna.gz --refList GCF_006335015.1_ASM633501v1_genomic.fna/target_genomes.txt --output GCF_006335015.1_ASM633501v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:55,721] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:55,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:55,723] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:55,736] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:55,737] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:55,737] [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 sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	100.0	2175	2179	95	conclusive
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	93.706	1818	2179	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	87.4509	1405	2179	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	87.2808	1595	2179	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.4227	995	2179	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.1172	1221	2179	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	80.9474	1215	2179	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	80.8346	1207	2179	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.6505	812	2179	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	78.6602	760	2179	95	below_threshold
Streptomyces torulosus	strain=NRRL B-3889	GCA_001419765.1	68276	68276	type	True	78.4296	823	2179	95	below_threshold
Streptomyces neyagawaensis	strain=JCM 4796	GCA_023516595.1	42238	42238	type	True	78.3997	910	2179	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	78.3193	935	2179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,739] [INFO] DFAST Taxonomy check result was written to GCF_006335015.1_ASM633501v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:55,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:55,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:55,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/checkm_data
[2024-01-24 12:22:55,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:55,809] [INFO] Task started: CheckM
[2024-01-24 12:22:55,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006335015.1_ASM633501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006335015.1_ASM633501v1_genomic.fna/checkm_input GCF_006335015.1_ASM633501v1_genomic.fna/checkm_result
[2024-01-24 12:24:01,848] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:01,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:01,877] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:01,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:01,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006335015.1_ASM633501v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:01,879] [INFO] Task started: Blastn
[2024-01-24 12:24:01,879] [INFO] Running command: blastn -query GCF_006335015.1_ASM633501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd139afe8-f2ed-424c-826d-4af5830c84fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_006335015.1_ASM633501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,966] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,970] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:03,970] [INFO] Target genome list was writen to GCF_006335015.1_ASM633501v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:03,977] [INFO] Task started: fastANI
[2024-01-24 12:24:03,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg84cc720c-db6c-4783-af59-78dd75cbe2f8/GCF_006335015.1_ASM633501v1_genomic.fna.gz --refList GCF_006335015.1_ASM633501v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006335015.1_ASM633501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:24,708] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:24,723] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:24,723] [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_006335015.1	s__Streptomyces sedi	100.0	2175	2179	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_900230195.1	s__Streptomyces zhaozhouensis	93.706	1818	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696235.1	s__Streptomyces triticirhizae	87.4355	1408	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	-
GCF_000974485.1	s__Streptomyces sp000974485	83.7428	1485	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.3947	999	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	81.3603	1092	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	81.1168	1222	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001984575.1	s__Streptomyces sp001984575	81.0901	1275	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003311645.1	s__Streptomyces sp003311645	80.9663	1205	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116145.1	s__Streptomyces harbinensis	80.9553	1072	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_000719135.1	s__Streptomyces avicenniae	80.6588	1094	2179	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:24,725] [INFO] GTDB search result was written to GCF_006335015.1_ASM633501v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:24,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:24,729] [INFO] DFAST_QC result json was written to GCF_006335015.1_ASM633501v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:24,729] [INFO] DFAST_QC completed!
[2024-01-24 12:24:24,729] [INFO] Total running time: 0h2m17s