[2023-06-08 09:05:13,015] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:13,017] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:13,018] [INFO] DQC Reference Directory: /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference
[2023-06-08 09:05:14,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:14,393] [INFO] Task started: Prodigal
[2023-06-08 09:05:14,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg962ad28e-dd4c-4aa9-9022-476b3292d258/GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:17,284] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:17,284] [INFO] Task started: HMMsearch
[2023-06-08 09:05:17,284] [INFO] Running command: hmmsearch --tblout GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/reference_markers.hmm GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:17,494] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:17,495] [INFO] Found 6/6 markers.
[2023-06-08 09:05:17,514] [INFO] Query marker FASTA was written to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:05:17,514] [INFO] Task started: Blastn
[2023-06-08 09:05:17,517] [INFO] Running command: blastn -query GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/reference_markers.fasta -out GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:18,202] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:18,206] [INFO] Selected 25 target genomes.
[2023-06-08 09:05:18,206] [INFO] Target genome list was writen to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:05:18,207] [INFO] Task started: fastANI
[2023-06-08 09:05:18,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg962ad28e-dd4c-4aa9-9022-476b3292d258/GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:33,429] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:33,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:33,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:33,432] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:33,432] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:05:33,432] [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
--------------------------------------------------------------------------------
[2023-06-08 09:05:33,434] [INFO] DFAST Taxonomy check result was written to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:05:33,434] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:33,434] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:33,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/checkm_data
[2023-06-08 09:05:33,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:33,453] [INFO] Task started: CheckM
[2023-06-08 09:05:33,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:05:50,148] [INFO] Task succeeded: CheckM
[2023-06-08 09:05:50,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:05:50,170] [INFO] ===== Completeness check finished =====
[2023-06-08 09:05:50,170] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:05:50,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:05:50,171] [INFO] Task started: Blastn
[2023-06-08 09:05:50,171] [INFO] Running command: blastn -query GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgacbc6da6-ccf6-4e2c-bfc6-93d337b1f2bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:51,269] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:51,274] [INFO] Selected 22 target genomes.
[2023-06-08 09:05:51,274] [INFO] Target genome list was writen to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:05:51,285] [INFO] Task started: fastANI
[2023-06-08 09:05:51,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg962ad28e-dd4c-4aa9-9022-476b3292d258/GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:05:57,080] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:57,087] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:05:57,087] [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_003539515.1	s__CAG-349 sp003539515	98.5294	343	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-349	95.0	97.82	96.90	0.94	0.89	17	conclusive
GCA_001940895.1	s__CAG-349 sp001940895	78.8549	116	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-917;g__CAG-349	95.0	98.38	97.95	0.83	0.78	4	-
--------------------------------------------------------------------------------
[2023-06-08 09:05:57,111] [INFO] GTDB search result was written to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:05:57,112] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:05:57,114] [INFO] DFAST_QC result json was written to GCA_945492565.1_SRR7188234_bin.12_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:05:57,114] [INFO] DFAST_QC completed!
[2023-06-08 09:05:57,115] [INFO] Total running time: 0h0m44s