[2023-06-13 17:12:17,016] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:12:17,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:12:17,018] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference
[2023-06-13 17:12:18,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:12:18,151] [INFO] Task started: Prodigal
[2023-06-13 17:12:18,151] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcab0a82-75a7-4ef6-98f4-cff8e0cf4490/GCA_022708085.1_ASM2270808v1_genomic.fna.gz | prodigal -d GCA_022708085.1_ASM2270808v1_genomic.fna/cds.fna -a GCA_022708085.1_ASM2270808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:12:26,565] [INFO] Task succeeded: Prodigal
[2023-06-13 17:12:26,565] [INFO] Task started: HMMsearch
[2023-06-13 17:12:26,566] [INFO] Running command: hmmsearch --tblout GCA_022708085.1_ASM2270808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/reference_markers.hmm GCA_022708085.1_ASM2270808v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:12:26,755] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:12:26,756] [INFO] Found 6/6 markers.
[2023-06-13 17:12:26,778] [INFO] Query marker FASTA was written to GCA_022708085.1_ASM2270808v1_genomic.fna/markers.fasta
[2023-06-13 17:12:26,778] [INFO] Task started: Blastn
[2023-06-13 17:12:26,778] [INFO] Running command: blastn -query GCA_022708085.1_ASM2270808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/reference_markers.fasta -out GCA_022708085.1_ASM2270808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:12:27,302] [INFO] Task succeeded: Blastn
[2023-06-13 17:12:27,305] [INFO] Selected 25 target genomes.
[2023-06-13 17:12:27,305] [INFO] Target genome list was writen to GCA_022708085.1_ASM2270808v1_genomic.fna/target_genomes.txt
[2023-06-13 17:12:27,312] [INFO] Task started: fastANI
[2023-06-13 17:12:27,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcab0a82-75a7-4ef6-98f4-cff8e0cf4490/GCA_022708085.1_ASM2270808v1_genomic.fna.gz --refList GCA_022708085.1_ASM2270808v1_genomic.fna/target_genomes.txt --output GCA_022708085.1_ASM2270808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:12:43,650] [INFO] Task succeeded: fastANI
[2023-06-13 17:12:43,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:12:43,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:12:43,664] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:12:43,664] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:12:43,664] [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
--------------------------------------------------------------------------------
[2023-06-13 17:12:43,666] [INFO] DFAST Taxonomy check result was written to GCA_022708085.1_ASM2270808v1_genomic.fna/tc_result.tsv
[2023-06-13 17:12:43,667] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:12:43,667] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:12:43,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/checkm_data
[2023-06-13 17:12:43,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:12:43,698] [INFO] Task started: CheckM
[2023-06-13 17:12:43,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708085.1_ASM2270808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708085.1_ASM2270808v1_genomic.fna/checkm_input GCA_022708085.1_ASM2270808v1_genomic.fna/checkm_result
[2023-06-13 17:13:11,482] [INFO] Task succeeded: CheckM
[2023-06-13 17:13:11,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:13:11,498] [INFO] ===== Completeness check finished =====
[2023-06-13 17:13:11,499] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:13:11,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708085.1_ASM2270808v1_genomic.fna/markers.fasta)
[2023-06-13 17:13:11,499] [INFO] Task started: Blastn
[2023-06-13 17:13:11,499] [INFO] Running command: blastn -query GCA_022708085.1_ASM2270808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcca1bb20-80c1-473a-8620-06b2c435054f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708085.1_ASM2270808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:13:12,217] [INFO] Task succeeded: Blastn
[2023-06-13 17:13:12,220] [INFO] Selected 25 target genomes.
[2023-06-13 17:13:12,220] [INFO] Target genome list was writen to GCA_022708085.1_ASM2270808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:13:12,281] [INFO] Task started: fastANI
[2023-06-13 17:13:12,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcab0a82-75a7-4ef6-98f4-cff8e0cf4490/GCA_022708085.1_ASM2270808v1_genomic.fna.gz --refList GCA_022708085.1_ASM2270808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708085.1_ASM2270808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:13:24,553] [INFO] Task succeeded: fastANI
[2023-06-13 17:13:24,558] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:13:24,558] [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
GCA_002069895.1	s__UBA5266 sp002069895	98.9914	422	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA5266	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002411545.1	s__UBA5266 sp002411545	82.2332	291	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA5266	95.0	99.03	98.53	0.75	0.73	4	-
GCA_017994425.1	s__UBA5266 sp017994425	78.7077	187	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA5266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012519525.1	s__UBA5266 sp012519525	76.7383	130	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA5266	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518765.1	s__UBA5266 sp012518765	76.2745	67	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__WCHB1-69;g__UBA5266	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:13:24,560] [INFO] GTDB search result was written to GCA_022708085.1_ASM2270808v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:13:24,560] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:13:24,562] [INFO] DFAST_QC result json was written to GCA_022708085.1_ASM2270808v1_genomic.fna/dqc_result.json
[2023-06-13 17:13:24,562] [INFO] DFAST_QC completed!
[2023-06-13 17:13:24,562] [INFO] Total running time: 0h1m8s