[2024-01-24 14:19:02,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,394] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference
[2024-01-24 14:19:03,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,637] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg92d3099d-b3b0-437a-80be-2d87a9caef59/GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/cds.fna -a GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:12,568] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:12,568] [INFO] Task started: HMMsearch
[2024-01-24 14:19:12,569] [INFO] Running command: hmmsearch --tblout GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/reference_markers.hmm GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:12,841] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:12,843] [INFO] Found 6/6 markers.
[2024-01-24 14:19:12,877] [INFO] Query marker FASTA was written to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:19:12,877] [INFO] Task started: Blastn
[2024-01-24 14:19:12,877] [INFO] Running command: blastn -query GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/reference_markers.fasta -out GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:13,543] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:13,546] [INFO] Selected 17 target genomes.
[2024-01-24 14:19:13,547] [INFO] Target genome list was writen to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:19:13,585] [INFO] Task started: fastANI
[2024-01-24 14:19:13,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d3099d-b3b0-437a-80be-2d87a9caef59/GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna.gz --refList GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:23,243] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:23,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:23,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:23,249] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:19:23,250] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:23,250] [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
Hydrogenoanaerobacterium saccharovorans	strain=CGMCC 1.5070	GCA_900110045.1	474960	474960	type	True	100.0	1054	1054	95	conclusive
Hydrogenoanaerobacterium saccharovorans	strain=DSM 24774	GCA_003814745.1	474960	474960	type	True	99.9967	1046	1054	95	conclusive
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	77.6948	92	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:23,252] [INFO] DFAST Taxonomy check result was written to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:19:23,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:23,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:23,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/checkm_data
[2024-01-24 14:19:23,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:23,290] [INFO] Task started: CheckM
[2024-01-24 14:19:23,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/checkm_input GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:19:55,925] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:55,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:55,950] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:55,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:55,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:19:55,951] [INFO] Task started: Blastn
[2024-01-24 14:19:55,951] [INFO] Running command: blastn -query GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5994a02-76a6-4ea4-bad7-3167e7894856/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:57,068] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:57,071] [INFO] Selected 25 target genomes.
[2024-01-24 14:19:57,072] [INFO] Target genome list was writen to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:57,094] [INFO] Task started: fastANI
[2024-01-24 14:19:57,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg92d3099d-b3b0-437a-80be-2d87a9caef59/GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna.gz --refList GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:08,075] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:08,079] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:08,079] [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_003814745.1	s__Hydrogenoanaerobacterium saccharovorans	99.9967	1046	1054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	77.6948	92	1054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,081] [INFO] GTDB search result was written to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:08,082] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:08,085] [INFO] DFAST_QC result json was written to GCF_900110045.1_IMG-taxon_2667527384_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:20:08,085] [INFO] DFAST_QC completed!
[2024-01-24 14:20:08,086] [INFO] Total running time: 0h1m6s