[2024-01-24 13:10:03,636] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:03,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:03,640] [INFO] DQC Reference Directory: /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference
[2024-01-24 13:10:05,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:05,025] [INFO] Task started: Prodigal
[2024-01-24 13:10:05,026] [INFO] Running command: gunzip -c /var/lib/cwl/stg2570255b-9c59-4f3f-8dca-9e06714e3196/GCF_000020965.1_ASM2096v1_genomic.fna.gz | prodigal -d GCF_000020965.1_ASM2096v1_genomic.fna/cds.fna -a GCF_000020965.1_ASM2096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:08,557] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:08,557] [INFO] Task started: HMMsearch
[2024-01-24 13:10:08,557] [INFO] Running command: hmmsearch --tblout GCF_000020965.1_ASM2096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/reference_markers.hmm GCF_000020965.1_ASM2096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:08,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:08,838] [INFO] Found 6/6 markers.
[2024-01-24 13:10:08,857] [INFO] Query marker FASTA was written to GCF_000020965.1_ASM2096v1_genomic.fna/markers.fasta
[2024-01-24 13:10:08,858] [INFO] Task started: Blastn
[2024-01-24 13:10:08,858] [INFO] Running command: blastn -query GCF_000020965.1_ASM2096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/reference_markers.fasta -out GCF_000020965.1_ASM2096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:09,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:09,428] [INFO] Selected 11 target genomes.
[2024-01-24 13:10:09,428] [INFO] Target genome list was writen to GCF_000020965.1_ASM2096v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:09,436] [INFO] Task started: fastANI
[2024-01-24 13:10:09,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg2570255b-9c59-4f3f-8dca-9e06714e3196/GCF_000020965.1_ASM2096v1_genomic.fna.gz --refList GCF_000020965.1_ASM2096v1_genomic.fna/target_genomes.txt --output GCF_000020965.1_ASM2096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:15,062] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:15,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:15,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:15,068] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:15,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:15,068] [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
Dictyoglomus thermophilum	strain=H-6-12; ATCC 35947	GCA_000020965.1	14	14	type	True	100.0	653	653	95	conclusive
Dictyoglomus turgidum	strain=DSM 6724	GCA_000021645.1	513050	513050	type	True	81.0795	480	653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,070] [INFO] DFAST Taxonomy check result was written to GCF_000020965.1_ASM2096v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:15,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:15,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:15,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/checkm_data
[2024-01-24 13:10:15,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:15,095] [INFO] Task started: CheckM
[2024-01-24 13:10:15,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020965.1_ASM2096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020965.1_ASM2096v1_genomic.fna/checkm_input GCF_000020965.1_ASM2096v1_genomic.fna/checkm_result
[2024-01-24 13:10:33,653] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:33,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:33,675] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:33,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:33,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020965.1_ASM2096v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:33,676] [INFO] Task started: Blastn
[2024-01-24 13:10:33,676] [INFO] Running command: blastn -query GCF_000020965.1_ASM2096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbcc098-8797-46ba-8fb7-9e27d851e559/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020965.1_ASM2096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:34,476] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:34,480] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:34,481] [INFO] Target genome list was writen to GCF_000020965.1_ASM2096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:34,514] [INFO] Task started: fastANI
[2024-01-24 13:10:34,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg2570255b-9c59-4f3f-8dca-9e06714e3196/GCF_000020965.1_ASM2096v1_genomic.fna.gz --refList GCF_000020965.1_ASM2096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020965.1_ASM2096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:40,135] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:40,143] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:40,143] [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_000020965.1	s__Dictyoglomus thermophilum	100.0	653	653	d__Bacteria;p__Dictyoglomota;c__Dictyoglomia;o__Dictyoglomales;f__Dictyoglomaceae;g__Dictyoglomus	95.0	98.74	98.68	0.94	0.91	5	conclusive
GCF_000021645.1	s__Dictyoglomus turgidum	81.0795	479	653	d__Bacteria;p__Dictyoglomota;c__Dictyoglomia;o__Dictyoglomales;f__Dictyoglomaceae;g__Dictyoglomus	95.0	99.82	99.66	0.95	0.90	3	-
GCF_008124665.1	s__OB1-4 sp008124665	77.5528	222	653	d__Bacteria;p__Dictyoglomota;c__Dictyoglomia;o__Dictyoglomales;f__Dictyoglomaceae;g__OB1-4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011333985.1	s__OB1-4 sp011333985	77.3997	206	653	d__Bacteria;p__Dictyoglomota;c__Dictyoglomia;o__Dictyoglomales;f__Dictyoglomaceae;g__OB1-4	95.0	99.81	99.81	0.96	0.96	2	-
GCA_002878375.1	s__NZ13-RE01 sp002878375	77.3485	82	653	d__Bacteria;p__Dictyoglomota;c__Dictyoglomia;o__Dictyoglomales;f__Dictyoglomaceae;g__NZ13-RE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:40,145] [INFO] GTDB search result was written to GCF_000020965.1_ASM2096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:40,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:40,148] [INFO] DFAST_QC result json was written to GCF_000020965.1_ASM2096v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:40,148] [INFO] DFAST_QC completed!
[2024-01-24 13:10:40,148] [INFO] Total running time: 0h0m37s