[2023-06-28 18:56:03,571] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:56:03,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:56:03,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference
[2023-06-28 18:56:04,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:56:04,894] [INFO] Task started: Prodigal
[2023-06-28 18:56:04,894] [INFO] Running command: gunzip -c /var/lib/cwl/stgbae21999-a739-4433-b2be-c62b33f9367e/GCA_020725545.1_ASM2072554v1_genomic.fna.gz | prodigal -d GCA_020725545.1_ASM2072554v1_genomic.fna/cds.fna -a GCA_020725545.1_ASM2072554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:56:13,546] [INFO] Task succeeded: Prodigal
[2023-06-28 18:56:13,546] [INFO] Task started: HMMsearch
[2023-06-28 18:56:13,547] [INFO] Running command: hmmsearch --tblout GCA_020725545.1_ASM2072554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/reference_markers.hmm GCA_020725545.1_ASM2072554v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:56:13,833] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:56:13,835] [INFO] Found 6/6 markers.
[2023-06-28 18:56:13,873] [INFO] Query marker FASTA was written to GCA_020725545.1_ASM2072554v1_genomic.fna/markers.fasta
[2023-06-28 18:56:13,874] [INFO] Task started: Blastn
[2023-06-28 18:56:13,874] [INFO] Running command: blastn -query GCA_020725545.1_ASM2072554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/reference_markers.fasta -out GCA_020725545.1_ASM2072554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:56:14,504] [INFO] Task succeeded: Blastn
[2023-06-28 18:56:14,509] [INFO] Selected 24 target genomes.
[2023-06-28 18:56:14,509] [INFO] Target genome list was writen to GCA_020725545.1_ASM2072554v1_genomic.fna/target_genomes.txt
[2023-06-28 18:56:14,519] [INFO] Task started: fastANI
[2023-06-28 18:56:14,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae21999-a739-4433-b2be-c62b33f9367e/GCA_020725545.1_ASM2072554v1_genomic.fna.gz --refList GCA_020725545.1_ASM2072554v1_genomic.fna/target_genomes.txt --output GCA_020725545.1_ASM2072554v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:56:32,251] [INFO] Task succeeded: fastANI
[2023-06-28 18:56:32,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:56:32,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:56:32,256] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:56:32,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:56:32,256] [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
Desulfobacca acetoxidans	strain=DSM 11109	GCA_000195295.1	60893	60893	type	True	77.2356	191	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:56:32,262] [INFO] DFAST Taxonomy check result was written to GCA_020725545.1_ASM2072554v1_genomic.fna/tc_result.tsv
[2023-06-28 18:56:32,262] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:56:32,263] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:56:32,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/checkm_data
[2023-06-28 18:56:32,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:56:32,303] [INFO] Task started: CheckM
[2023-06-28 18:56:32,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020725545.1_ASM2072554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020725545.1_ASM2072554v1_genomic.fna/checkm_input GCA_020725545.1_ASM2072554v1_genomic.fna/checkm_result
[2023-06-28 18:57:02,481] [INFO] Task succeeded: CheckM
[2023-06-28 18:57:02,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:57:02,509] [INFO] ===== Completeness check finished =====
[2023-06-28 18:57:02,510] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:57:02,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020725545.1_ASM2072554v1_genomic.fna/markers.fasta)
[2023-06-28 18:57:02,511] [INFO] Task started: Blastn
[2023-06-28 18:57:02,511] [INFO] Running command: blastn -query GCA_020725545.1_ASM2072554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc220bf50-23da-4937-8ba2-ddc6f9bbf8db/dqc_reference/reference_markers_gtdb.fasta -out GCA_020725545.1_ASM2072554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:57:03,518] [INFO] Task succeeded: Blastn
[2023-06-28 18:57:03,525] [INFO] Selected 21 target genomes.
[2023-06-28 18:57:03,525] [INFO] Target genome list was writen to GCA_020725545.1_ASM2072554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:57:03,544] [INFO] Task started: fastANI
[2023-06-28 18:57:03,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae21999-a739-4433-b2be-c62b33f9367e/GCA_020725545.1_ASM2072554v1_genomic.fna.gz --refList GCA_020725545.1_ASM2072554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020725545.1_ASM2072554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:57:17,785] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:17,798] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:57:17,798] [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_016874895.1	s__Desulfobacca sp016874895	77.9002	294	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__Desulfobaccaceae;g__Desulfobacca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195295.1	s__Desulfobacca acetoxidans	77.2356	191	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__Desulfobaccaceae;g__Desulfobacca	95.0	98.48	98.47	0.87	0.83	3	-
GCA_016874915.1	s__0-14-0-80-60-11 sp016874915	76.7239	126	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875015.1	s__0-14-0-80-60-11 sp016875015	76.7201	120	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599195.1	s__SURF-52 sp003599195	76.7181	124	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__SURF-52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874945.1	s__0-14-0-80-60-11 sp016874945	76.6321	105	959	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:57:17,801] [INFO] GTDB search result was written to GCA_020725545.1_ASM2072554v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:57:17,801] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:57:17,804] [INFO] DFAST_QC result json was written to GCA_020725545.1_ASM2072554v1_genomic.fna/dqc_result.json
[2023-06-28 18:57:17,804] [INFO] DFAST_QC completed!
[2023-06-28 18:57:17,804] [INFO] Total running time: 0h1m14s