[2024-01-24 14:28:02,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference
[2024-01-24 14:28:04,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:04,054] [INFO] Task started: Prodigal
[2024-01-24 14:28:04,055] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf45cbcd-b2a2-4eef-89cc-9ff91d68c35a/GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/cds.fna -a GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:24,866] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:24,866] [INFO] Task started: HMMsearch
[2024-01-24 14:28:24,866] [INFO] Running command: hmmsearch --tblout GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/reference_markers.hmm GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:25,306] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:25,307] [INFO] Found 6/6 markers.
[2024-01-24 14:28:25,379] [INFO] Query marker FASTA was written to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:28:25,380] [INFO] Task started: Blastn
[2024-01-24 14:28:25,380] [INFO] Running command: blastn -query GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/reference_markers.fasta -out GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:26,827] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:26,830] [INFO] Selected 17 target genomes.
[2024-01-24 14:28:26,831] [INFO] Target genome list was writen to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:28:26,860] [INFO] Task started: fastANI
[2024-01-24 14:28:26,860] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf45cbcd-b2a2-4eef-89cc-9ff91d68c35a/GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna.gz --refList GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:29:07,113] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:07,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:29:07,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:29:07,130] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:29:07,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:29:07,130] [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
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	100.0	2559	2559	95	conclusive
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	99.9848	2533	2559	95	conclusive
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	93.4166	1995	2559	95	below_threshold
Jiangella endophytica	strain=KE2-3	GCA_003427025.1	1623398	1623398	type	True	89.8963	1929	2559	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	89.385	1780	2559	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	89.348	1830	2559	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	88.9663	1546	2559	95	below_threshold
Jiangella anatolica	strain=GTF31	GCA_003236295.1	2670374	2670374	type	True	88.6624	1673	2559	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	87.5916	1738	2559	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	87.4338	1588	2559	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	83.4206	1337	2559	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	83.3935	1403	2559	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	76.5322	538	2559	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	76.3152	966	2559	95	below_threshold
Actinoallomurus purpureus	strain=KCTC 19541	GCA_024055795.1	478114	478114	type	True	76.2846	706	2559	95	below_threshold
Actinomadura graeca	strain=32-07	GCA_019175365.1	2750812	2750812	type	True	76.1618	800	2559	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.1001	766	2559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:29:07,132] [INFO] DFAST Taxonomy check result was written to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:29:07,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:29:07,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:29:07,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/checkm_data
[2024-01-24 14:29:07,134] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:29:07,203] [INFO] Task started: CheckM
[2024-01-24 14:29:07,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/checkm_input GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:30:54,921] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:54,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:54,945] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:54,946] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:54,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:30:54,947] [INFO] Task started: Blastn
[2024-01-24 14:30:54,947] [INFO] Running command: blastn -query GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg87543d77-c6b4-42d6-bd3f-900ae7441485/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:57,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:57,219] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:57,220] [INFO] Target genome list was writen to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:57,232] [INFO] Task started: fastANI
[2024-01-24 14:30:57,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf45cbcd-b2a2-4eef-89cc-9ff91d68c35a/GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna.gz --refList GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:22,606] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:22,615] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:22,615] [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_900106035.1	s__Jiangella alba	100.0	2559	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	conclusive
GCF_001270745.1	s__Jiangella muralis	93.3871	1998	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003427025.1	s__Jiangella endophytica	89.8661	1933	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	89.3061	1836	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003579925.1	s__Jiangella rhizosphaerae	88.9126	1553	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236295.1	s__Jiangella anatolica	88.7048	1666	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204975.1	s__Jiangella mangrovi	87.6621	1729	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	87.4501	1587	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515395.1	s__Jiangella gansuensis	83.4552	1332	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	83.405	1401	2559	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:22,617] [INFO] GTDB search result was written to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:22,617] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:22,621] [INFO] DFAST_QC result json was written to GCF_900106035.1_IMG-taxon_2630968302_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:31:22,621] [INFO] DFAST_QC completed!
[2024-01-24 14:31:22,621] [INFO] Total running time: 0h3m20s