[2023-06-07 21:13:35,666] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:35,667] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:35,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference
[2023-06-07 21:13:37,123] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:37,124] [INFO] Task started: Prodigal
[2023-06-07 21:13:37,124] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fef5c3f-a1de-4d2c-bf49-3a9629a5cb3a/GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:41,788] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:41,788] [INFO] Task started: HMMsearch
[2023-06-07 21:13:41,788] [INFO] Running command: hmmsearch --tblout GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/reference_markers.hmm GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:42,037] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:42,038] [INFO] Found 6/6 markers.
[2023-06-07 21:13:42,062] [INFO] Query marker FASTA was written to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 21:13:42,062] [INFO] Task started: Blastn
[2023-06-07 21:13:42,062] [INFO] Running command: blastn -query GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/reference_markers.fasta -out GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:42,617] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:42,621] [INFO] Selected 17 target genomes.
[2023-06-07 21:13:42,621] [INFO] Target genome list was writen to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 21:13:42,623] [INFO] Task started: fastANI
[2023-06-07 21:13:42,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fef5c3f-a1de-4d2c-bf49-3a9629a5cb3a/GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:13:54,573] [INFO] Task succeeded: fastANI
[2023-06-07 21:13:54,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:13:54,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:13:54,576] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:13:54,576] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-07 21:13:54,577] [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
--------------------------------------------------------------------------------
[2023-06-07 21:13:54,579] [INFO] DFAST Taxonomy check result was written to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 21:13:54,579] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:13:54,580] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:13:54,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/checkm_data
[2023-06-07 21:13:54,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:13:54,613] [INFO] Task started: CheckM
[2023-06-07 21:13:54,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 21:14:16,272] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:16,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:16,293] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:16,293] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:16,293] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 21:14:16,294] [INFO] Task started: Blastn
[2023-06-07 21:14:16,294] [INFO] Running command: blastn -query GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg630a2e09-25d8-448a-9796-6bce0f6eb84d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:17,039] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:17,043] [INFO] Selected 25 target genomes.
[2023-06-07 21:14:17,043] [INFO] Target genome list was writen to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:17,062] [INFO] Task started: fastANI
[2023-06-07 21:14:17,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fef5c3f-a1de-4d2c-bf49-3a9629a5cb3a/GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:14:25,328] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:25,335] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:14:25,336] [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_018883625.1	s__Treponema_F excrementipullorum	97.5172	479	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016294105.1	s__Treponema_F sp016294105	77.1452	75	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	97.89	97.89	0.95	0.95	2	-
GCA_017629095.1	s__Treponema_F sp017629095	76.8116	63	646	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_F	95.0	97.22	97.22	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-07 21:14:25,338] [INFO] GTDB search result was written to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 21:14:25,338] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:14:25,340] [INFO] DFAST_QC result json was written to GCA_945937085.1_SRR15057926_bin.4_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 21:14:25,340] [INFO] DFAST_QC completed!
[2023-06-07 21:14:25,340] [INFO] Total running time: 0h0m50s