[2023-06-30 01:13:09,165] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:13:09,167] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:13:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference
[2023-06-30 01:13:10,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:13:10,407] [INFO] Task started: Prodigal
[2023-06-30 01:13:10,407] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4b82682-48f0-4d52-8415-e03ba009c8a8/GCA_016283735.1_ASM1628373v1_genomic.fna.gz | prodigal -d GCA_016283735.1_ASM1628373v1_genomic.fna/cds.fna -a GCA_016283735.1_ASM1628373v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:13:25,220] [INFO] Task succeeded: Prodigal
[2023-06-30 01:13:25,220] [INFO] Task started: HMMsearch
[2023-06-30 01:13:25,220] [INFO] Running command: hmmsearch --tblout GCA_016283735.1_ASM1628373v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/reference_markers.hmm GCA_016283735.1_ASM1628373v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:13:25,480] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:13:25,482] [INFO] Found 6/6 markers.
[2023-06-30 01:13:25,509] [INFO] Query marker FASTA was written to GCA_016283735.1_ASM1628373v1_genomic.fna/markers.fasta
[2023-06-30 01:13:25,510] [INFO] Task started: Blastn
[2023-06-30 01:13:25,510] [INFO] Running command: blastn -query GCA_016283735.1_ASM1628373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/reference_markers.fasta -out GCA_016283735.1_ASM1628373v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:13:26,114] [INFO] Task succeeded: Blastn
[2023-06-30 01:13:26,120] [INFO] Selected 26 target genomes.
[2023-06-30 01:13:26,120] [INFO] Target genome list was writen to GCA_016283735.1_ASM1628373v1_genomic.fna/target_genomes.txt
[2023-06-30 01:13:26,125] [INFO] Task started: fastANI
[2023-06-30 01:13:26,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b82682-48f0-4d52-8415-e03ba009c8a8/GCA_016283735.1_ASM1628373v1_genomic.fna.gz --refList GCA_016283735.1_ASM1628373v1_genomic.fna/target_genomes.txt --output GCA_016283735.1_ASM1628373v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:13:41,757] [INFO] Task succeeded: fastANI
[2023-06-30 01:13:41,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:13:41,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:13:41,766] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:13:41,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 01:13:41,767] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	76.5706	98	828	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	76.5622	96	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 01:13:41,769] [INFO] DFAST Taxonomy check result was written to GCA_016283735.1_ASM1628373v1_genomic.fna/tc_result.tsv
[2023-06-30 01:13:41,770] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:13:41,770] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:13:41,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/checkm_data
[2023-06-30 01:13:41,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:13:41,803] [INFO] Task started: CheckM
[2023-06-30 01:13:41,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016283735.1_ASM1628373v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016283735.1_ASM1628373v1_genomic.fna/checkm_input GCA_016283735.1_ASM1628373v1_genomic.fna/checkm_result
[2023-06-30 01:14:27,604] [INFO] Task succeeded: CheckM
[2023-06-30 01:14:27,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:14:27,625] [INFO] ===== Completeness check finished =====
[2023-06-30 01:14:27,625] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:14:27,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016283735.1_ASM1628373v1_genomic.fna/markers.fasta)
[2023-06-30 01:14:27,626] [INFO] Task started: Blastn
[2023-06-30 01:14:27,626] [INFO] Running command: blastn -query GCA_016283735.1_ASM1628373v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61971d0-0b2a-43e7-b611-127b21d86780/dqc_reference/reference_markers_gtdb.fasta -out GCA_016283735.1_ASM1628373v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:14:28,433] [INFO] Task succeeded: Blastn
[2023-06-30 01:14:28,438] [INFO] Selected 12 target genomes.
[2023-06-30 01:14:28,438] [INFO] Target genome list was writen to GCA_016283735.1_ASM1628373v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:14:28,444] [INFO] Task started: fastANI
[2023-06-30 01:14:28,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4b82682-48f0-4d52-8415-e03ba009c8a8/GCA_016283735.1_ASM1628373v1_genomic.fna.gz --refList GCA_016283735.1_ASM1628373v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016283735.1_ASM1628373v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:14:36,685] [INFO] Task succeeded: fastANI
[2023-06-30 01:14:36,700] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:14:36,701] [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_902785925.1	s__Sodaliphilus sp902785925	96.9992	717	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.61	97.00	0.89	0.87	5	conclusive
GCA_902792435.1	s__Sodaliphilus sp902792435	83.6152	525	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.75	96.43	0.87	0.84	5	-
GCA_902762385.1	s__Sodaliphilus sp902762385	83.3074	558	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.01	95.72	0.89	0.77	6	-
GCA_002353285.1	s__Sodaliphilus sp002353285	81.3825	372	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.36	97.36	0.78	0.78	2	-
GCA_900318065.1	s__Sodaliphilus sp900318065	81.252	459	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_017451225.1	s__Sodaliphilus sp017451225	81.1719	351	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233845.1	s__Sodaliphilus sp905233845	80.4019	436	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548365.1	s__Sodaliphilus sp017548365	80.2427	412	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318255.1	s__Sodaliphilus sp900318255	80.1446	405	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_017964485.1	s__Sodaliphilus sp017964485	79.9249	372	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.79	96.79	0.86	0.86	2	-
GCA_017618355.1	s__Sodaliphilus sp017618355	79.8176	358	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557625.1	s__Sodaliphilus sp017557625	79.712	368	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 01:14:36,703] [INFO] GTDB search result was written to GCA_016283735.1_ASM1628373v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:14:36,703] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:14:36,706] [INFO] DFAST_QC result json was written to GCA_016283735.1_ASM1628373v1_genomic.fna/dqc_result.json
[2023-06-30 01:14:36,707] [INFO] DFAST_QC completed!
[2023-06-30 01:14:36,707] [INFO] Total running time: 0h1m28s