[2024-01-24 14:39:44,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:44,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:44,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference
[2024-01-24 14:39:45,970] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:45,971] [INFO] Task started: Prodigal
[2024-01-24 14:39:45,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2f2984f-73ff-409f-a0e6-0c3f2e0822d1/GCF_001570525.1_ASM157052v1_genomic.fna.gz | prodigal -d GCF_001570525.1_ASM157052v1_genomic.fna/cds.fna -a GCF_001570525.1_ASM157052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:15,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:15,883] [INFO] Task started: HMMsearch
[2024-01-24 14:40:15,883] [INFO] Running command: hmmsearch --tblout GCF_001570525.1_ASM157052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/reference_markers.hmm GCF_001570525.1_ASM157052v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:16,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:16,287] [INFO] Found 6/6 markers.
[2024-01-24 14:40:16,358] [INFO] Query marker FASTA was written to GCF_001570525.1_ASM157052v1_genomic.fna/markers.fasta
[2024-01-24 14:40:16,358] [INFO] Task started: Blastn
[2024-01-24 14:40:16,358] [INFO] Running command: blastn -query GCF_001570525.1_ASM157052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/reference_markers.fasta -out GCF_001570525.1_ASM157052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:17,707] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:17,710] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:17,710] [INFO] Target genome list was writen to GCF_001570525.1_ASM157052v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:17,720] [INFO] Task started: fastANI
[2024-01-24 14:40:17,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2f2984f-73ff-409f-a0e6-0c3f2e0822d1/GCF_001570525.1_ASM157052v1_genomic.fna.gz --refList GCF_001570525.1_ASM157052v1_genomic.fna/target_genomes.txt --output GCF_001570525.1_ASM157052v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:44,888] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:44,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:44,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:44,898] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:44,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:44,899] [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
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	100.0	2839	2847	95	conclusive
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	93.6264	2325	2847	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	93.39	2330	2847	95	below_threshold
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	90.1681	2265	2847	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	89.2535	2303	2847	95	below_threshold
Planobispora takensis	strain=NBRC 109077	GCA_016863195.1	1367882	1367882	type	True	79.7108	1288	2847	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.7069	1184	2847	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.4412	899	2847	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.3166	1344	2847	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.0854	1265	2847	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.9454	1280	2847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:44,900] [INFO] DFAST Taxonomy check result was written to GCF_001570525.1_ASM157052v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:44,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:44,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:44,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/checkm_data
[2024-01-24 14:40:44,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:44,979] [INFO] Task started: CheckM
[2024-01-24 14:40:44,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001570525.1_ASM157052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001570525.1_ASM157052v1_genomic.fna/checkm_input GCF_001570525.1_ASM157052v1_genomic.fna/checkm_result
[2024-01-24 14:42:16,552] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:16,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:16,575] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:16,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:16,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001570525.1_ASM157052v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:16,576] [INFO] Task started: Blastn
[2024-01-24 14:42:16,576] [INFO] Running command: blastn -query GCF_001570525.1_ASM157052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ff7648a-e8ae-4114-bed8-0e8d9cf1681f/dqc_reference/reference_markers_gtdb.fasta -out GCF_001570525.1_ASM157052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:18,924] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:18,928] [INFO] Selected 6 target genomes.
[2024-01-24 14:42:18,928] [INFO] Target genome list was writen to GCF_001570525.1_ASM157052v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:18,933] [INFO] Task started: fastANI
[2024-01-24 14:42:18,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2f2984f-73ff-409f-a0e6-0c3f2e0822d1/GCF_001570525.1_ASM157052v1_genomic.fna.gz --refList GCF_001570525.1_ASM157052v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001570525.1_ASM157052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:35,370] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:35,379] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:35,380] [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_001570525.1	s__Herbidospora sakaeratensis	100.0	2839	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001570585.1	s__Herbidospora daliensis	94.591	2459	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233835.1	s__Herbidospora galbida	93.6204	2325	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009901565.1	s__Herbidospora solisilvae	93.3974	2329	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	95.93	95.93	0.91	0.91	2	-
GCF_001570565.1	s__Herbidospora yilanensis	93.3173	2258	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017896165.1	s__Microbispora sp017896165	79.7606	1171	2847	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:35,381] [INFO] GTDB search result was written to GCF_001570525.1_ASM157052v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:35,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:35,385] [INFO] DFAST_QC result json was written to GCF_001570525.1_ASM157052v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:35,385] [INFO] DFAST_QC completed!
[2024-01-24 14:42:35,385] [INFO] Total running time: 0h2m51s