[2024-01-24 14:22:03,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:03,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:03,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference
[2024-01-24 14:22:04,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:04,725] [INFO] Task started: Prodigal
[2024-01-24 14:22:04,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd4957aa-48f8-4a55-8b4f-1594e01ae1ee/GCF_005233835.1_ASM523383v1_genomic.fna.gz | prodigal -d GCF_005233835.1_ASM523383v1_genomic.fna/cds.fna -a GCF_005233835.1_ASM523383v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:26,507] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:26,508] [INFO] Task started: HMMsearch
[2024-01-24 14:22:26,508] [INFO] Running command: hmmsearch --tblout GCF_005233835.1_ASM523383v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/reference_markers.hmm GCF_005233835.1_ASM523383v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:26,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:26,934] [INFO] Found 6/6 markers.
[2024-01-24 14:22:27,006] [INFO] Query marker FASTA was written to GCF_005233835.1_ASM523383v1_genomic.fna/markers.fasta
[2024-01-24 14:22:27,006] [INFO] Task started: Blastn
[2024-01-24 14:22:27,006] [INFO] Running command: blastn -query GCF_005233835.1_ASM523383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/reference_markers.fasta -out GCF_005233835.1_ASM523383v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:28,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:28,421] [INFO] Selected 12 target genomes.
[2024-01-24 14:22:28,422] [INFO] Target genome list was writen to GCF_005233835.1_ASM523383v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:28,431] [INFO] Task started: fastANI
[2024-01-24 14:22:28,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd4957aa-48f8-4a55-8b4f-1594e01ae1ee/GCF_005233835.1_ASM523383v1_genomic.fna.gz --refList GCF_005233835.1_ASM523383v1_genomic.fna/target_genomes.txt --output GCF_005233835.1_ASM523383v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:55,506] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:55,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:55,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:55,525] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:55,525] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:55,525] [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 galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	100.0	2705	2713	95	conclusive
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	93.7109	2286	2713	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	93.6646	2336	2713	95	below_threshold
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	90.5966	2170	2713	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	89.9795	2220	2713	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	80.1397	1265	2713	95	below_threshold
Microbispora oryzae	strain=RL4-1S	GCA_017896165.1	2806554	2806554	type	True	79.8059	1157	2713	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	79.5203	1176	2713	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	79.4633	856	2713	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	79.415	1274	2713	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	79.1437	1241	2713	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	78.778	1241	2713	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:55,527] [INFO] DFAST Taxonomy check result was written to GCF_005233835.1_ASM523383v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:55,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:55,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:55,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/checkm_data
[2024-01-24 14:22:55,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:55,601] [INFO] Task started: CheckM
[2024-01-24 14:22:55,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005233835.1_ASM523383v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005233835.1_ASM523383v1_genomic.fna/checkm_input GCF_005233835.1_ASM523383v1_genomic.fna/checkm_result
[2024-01-24 14:24:01,722] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:01,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:01,749] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:01,750] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:01,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005233835.1_ASM523383v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:01,750] [INFO] Task started: Blastn
[2024-01-24 14:24:01,751] [INFO] Running command: blastn -query GCF_005233835.1_ASM523383v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97b2d50a-0551-4c17-8760-165dfa82a13c/dqc_reference/reference_markers_gtdb.fasta -out GCF_005233835.1_ASM523383v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:03,876] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:03,881] [INFO] Selected 7 target genomes.
[2024-01-24 14:24:03,881] [INFO] Target genome list was writen to GCF_005233835.1_ASM523383v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:03,886] [INFO] Task started: fastANI
[2024-01-24 14:24:03,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd4957aa-48f8-4a55-8b4f-1594e01ae1ee/GCF_005233835.1_ASM523383v1_genomic.fna.gz --refList GCF_005233835.1_ASM523383v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005233835.1_ASM523383v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:21,227] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:21,235] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:21,235] [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_005233835.1	s__Herbidospora galbida	100.0	2705	2713	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_001570565.1	s__Herbidospora yilanensis	93.7466	2179	2713	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	93.7194	2285	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	95.93	95.93	0.91	0.91	2	-
GCF_001570525.1	s__Herbidospora sakaeratensis	93.6657	2336	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570585.1	s__Herbidospora daliensis	93.3878	2367	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570545.1	s__Herbidospora mongoliensis	90.0096	2214	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Herbidospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863035.1	s__Microbispora corallina	80.1277	1268	2713	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microbispora	95.0	97.01	97.01	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:21,237] [INFO] GTDB search result was written to GCF_005233835.1_ASM523383v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:21,237] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:21,241] [INFO] DFAST_QC result json was written to GCF_005233835.1_ASM523383v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:21,241] [INFO] DFAST_QC completed!
[2024-01-24 14:24:21,241] [INFO] Total running time: 0h2m18s