[2024-01-24 14:14:01,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:01,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:01,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference
[2024-01-24 14:14:02,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,310] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f6a1bd6-e7a1-4cdd-8178-842aed1ec927/GCF_012034175.1_ASM1203417v1_genomic.fna.gz | prodigal -d GCF_012034175.1_ASM1203417v1_genomic.fna/cds.fna -a GCF_012034175.1_ASM1203417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:30,902] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:30,903] [INFO] Task started: HMMsearch
[2024-01-24 14:14:30,903] [INFO] Running command: hmmsearch --tblout GCF_012034175.1_ASM1203417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/reference_markers.hmm GCF_012034175.1_ASM1203417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:31,514] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:31,515] [INFO] Found 6/6 markers.
[2024-01-24 14:14:31,606] [INFO] Query marker FASTA was written to GCF_012034175.1_ASM1203417v1_genomic.fna/markers.fasta
[2024-01-24 14:14:31,607] [INFO] Task started: Blastn
[2024-01-24 14:14:31,607] [INFO] Running command: blastn -query GCF_012034175.1_ASM1203417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/reference_markers.fasta -out GCF_012034175.1_ASM1203417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:33,492] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:33,497] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:33,497] [INFO] Target genome list was writen to GCF_012034175.1_ASM1203417v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:33,508] [INFO] Task started: fastANI
[2024-01-24 14:14:33,508] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6a1bd6-e7a1-4cdd-8178-842aed1ec927/GCF_012034175.1_ASM1203417v1_genomic.fna.gz --refList GCF_012034175.1_ASM1203417v1_genomic.fna/target_genomes.txt --output GCF_012034175.1_ASM1203417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:08,149] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:08,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:08,164] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:08,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:08,164] [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
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	100.0	2703	2707	95	conclusive
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	86.3715	1511	2707	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	86.2028	1785	2707	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	86.1793	1787	2707	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.3639	1560	2707	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.1474	1563	2707	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	82.8438	1599	2707	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	80.0523	1103	2707	95	below_threshold
Streptomyces angustmyceticus	strain=JCM 4053	GCA_019933235.1	285578	285578	type	True	79.9713	1188	2707	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	79.8057	1215	2707	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	79.747	1153	2707	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	79.6781	1139	2707	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.6647	1290	2707	95	below_threshold
Streptomyces microflavus	strain=JCM 4496	GCA_014650075.1	1919	1919	type	True	79.6387	1148	2707	95	below_threshold
Streptomyces camponoticapitis	strain=CGMCC 4.7275	GCA_014646115.1	1616125	1616125	type	True	79.5962	1091	2707	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	79.465	1306	2707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,190] [INFO] DFAST Taxonomy check result was written to GCF_012034175.1_ASM1203417v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:08,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:08,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:08,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/checkm_data
[2024-01-24 14:15:08,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:08,288] [INFO] Task started: CheckM
[2024-01-24 14:15:08,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012034175.1_ASM1203417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012034175.1_ASM1203417v1_genomic.fna/checkm_input GCF_012034175.1_ASM1203417v1_genomic.fna/checkm_result
[2024-01-24 14:16:56,950] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:56,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:56,979] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:56,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:56,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012034175.1_ASM1203417v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:56,980] [INFO] Task started: Blastn
[2024-01-24 14:16:56,980] [INFO] Running command: blastn -query GCF_012034175.1_ASM1203417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8510c36a-7fb0-4fb0-854b-946fa20ab106/dqc_reference/reference_markers_gtdb.fasta -out GCF_012034175.1_ASM1203417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:59,217] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:59,220] [INFO] Selected 10 target genomes.
[2024-01-24 14:16:59,221] [INFO] Target genome list was writen to GCF_012034175.1_ASM1203417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:59,229] [INFO] Task started: fastANI
[2024-01-24 14:16:59,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6a1bd6-e7a1-4cdd-8178-842aed1ec927/GCF_012034175.1_ASM1203417v1_genomic.fna.gz --refList GCF_012034175.1_ASM1203417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012034175.1_ASM1203417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:23,429] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:23,446] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:23,447] [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_012034175.1	s__Streptomyces sp012034175	100.0	2703	2707	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_000721495.1	s__Streptomyces sp000721495	86.8987	1841	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	86.2326	1781	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900142575.1	s__Streptomyces paucisporeus	86.1878	1786	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	85.7317	1675	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596445.1	s__Streptomyces sp014596445	83.2794	1464	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003999195.1	s__Streptomyces sp003999195	80.528	1191	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018866325.1	s__Streptomyces sp001895105	79.6896	1111	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.85	98.85	0.87	0.87	2	-
GCF_014650075.1	s__Streptomyces microflavus	79.6166	1154	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.25	97.27	0.91	0.85	13	-
GCF_001905345.1	s__Streptomyces uncialis	79.0905	1112	2707	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.41	97.41	0.92	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:23,449] [INFO] GTDB search result was written to GCF_012034175.1_ASM1203417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:23,449] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:23,455] [INFO] DFAST_QC result json was written to GCF_012034175.1_ASM1203417v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:23,455] [INFO] DFAST_QC completed!
[2024-01-24 14:17:23,455] [INFO] Total running time: 0h3m22s