[2024-01-24 12:47:05,724] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,726] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,726] [INFO] DQC Reference Directory: /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference
[2024-01-24 12:47:06,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,968] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,968] [INFO] Running command: gunzip -c /var/lib/cwl/stg5184276f-7f96-4b36-8d44-ff936b2d6e38/GCF_003626535.1_ASM362653v1_genomic.fna.gz | prodigal -d GCF_003626535.1_ASM362653v1_genomic.fna/cds.fna -a GCF_003626535.1_ASM362653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:30,548] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:30,548] [INFO] Task started: HMMsearch
[2024-01-24 12:47:30,548] [INFO] Running command: hmmsearch --tblout GCF_003626535.1_ASM362653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/reference_markers.hmm GCF_003626535.1_ASM362653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:30,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:30,846] [INFO] Found 6/6 markers.
[2024-01-24 12:47:30,900] [INFO] Query marker FASTA was written to GCF_003626535.1_ASM362653v1_genomic.fna/markers.fasta
[2024-01-24 12:47:30,900] [INFO] Task started: Blastn
[2024-01-24 12:47:30,900] [INFO] Running command: blastn -query GCF_003626535.1_ASM362653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/reference_markers.fasta -out GCF_003626535.1_ASM362653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:32,244] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:32,249] [INFO] Selected 17 target genomes.
[2024-01-24 12:47:32,249] [INFO] Target genome list was writen to GCF_003626535.1_ASM362653v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:32,256] [INFO] Task started: fastANI
[2024-01-24 12:47:32,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg5184276f-7f96-4b36-8d44-ff936b2d6e38/GCF_003626535.1_ASM362653v1_genomic.fna.gz --refList GCF_003626535.1_ASM362653v1_genomic.fna/target_genomes.txt --output GCF_003626535.1_ASM362653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:03,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:03,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:03,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:03,240] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:03,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:03,240] [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 hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	100.0	2391	2394	95	conclusive
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.7242	1170	2394	95	below_threshold
Streptomyces specialis	strain=type strain: GW41-1564	GCA_001493375.1	498367	498367	type	True	81.7098	1096	2394	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.4301	1280	2394	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.2455	1291	2394	95	below_threshold
Streptomyces triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	81.1146	1139	2394	95	below_threshold
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	81.1095	1197	2394	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	81.0192	1300	2394	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	80.9934	1180	2394	95	below_threshold
Streptomyces xiamenensis	strain=318	GCA_000993785.3	408015	408015	type	True	80.5503	1089	2394	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	79.8471	1035	2394	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	79.1949	949	2394	95	below_threshold
Streptomyces echinoruber	strain=JCM 5016	GCA_014651135.1	68898	68898	type	True	79.0764	1026	2394	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.0259	1033	2394	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	78.9078	1004	2394	95	below_threshold
Streptomyces jietaisiensis	strain=CGMCC 4.1859	GCA_900102095.1	235987	235987	type	True	78.8172	1041	2394	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.7707	1059	2394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:03,242] [INFO] DFAST Taxonomy check result was written to GCF_003626535.1_ASM362653v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:03,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:03,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:03,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/checkm_data
[2024-01-24 12:48:03,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:03,327] [INFO] Task started: CheckM
[2024-01-24 12:48:03,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003626535.1_ASM362653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003626535.1_ASM362653v1_genomic.fna/checkm_input GCF_003626535.1_ASM362653v1_genomic.fna/checkm_result
[2024-01-24 12:49:43,011] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:43,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:43,037] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:43,037] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:43,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003626535.1_ASM362653v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:43,037] [INFO] Task started: Blastn
[2024-01-24 12:49:43,038] [INFO] Running command: blastn -query GCF_003626535.1_ASM362653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36e9c912-1ca5-477d-9cee-6f8a42455e2b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003626535.1_ASM362653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:45,110] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:45,114] [INFO] Selected 13 target genomes.
[2024-01-24 12:49:45,114] [INFO] Target genome list was writen to GCF_003626535.1_ASM362653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:45,122] [INFO] Task started: fastANI
[2024-01-24 12:49:45,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg5184276f-7f96-4b36-8d44-ff936b2d6e38/GCF_003626535.1_ASM362653v1_genomic.fna.gz --refList GCF_003626535.1_ASM362653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003626535.1_ASM362653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:10,116] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:10,127] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:10,127] [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_003626535.1	s__Streptomyces hoynatensis	100.0	2391	2394	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_004348315.1	s__Streptomyces sp004348315	82.0611	1216	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.7596	1164	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	81.7528	1244	2394	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	81.691	1099	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984575.1	s__Streptomyces sp001984575	81.5483	1390	2394	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	81.4309	1226	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002128305.1	s__Streptomyces sp002128305	81.3648	1239	2394	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	81.239	1291	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004193175.1	s__Streptomyces sp004193175	81.162	1199	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719135.1	s__Streptomyces avicenniae	81.084	1216	2394	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	80.7848	1105	2394	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.20	99.18	0.96	0.96	3	-
GCF_000974485.1	s__Streptomyces sp000974485	80.4863	1201	2394	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 12:50:10,128] [INFO] GTDB search result was written to GCF_003626535.1_ASM362653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:10,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:10,132] [INFO] DFAST_QC result json was written to GCF_003626535.1_ASM362653v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:10,132] [INFO] DFAST_QC completed!
[2024-01-24 12:50:10,132] [INFO] Total running time: 0h3m4s