[2023-06-28 18:27:09,881] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:09,883] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:09,883] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference
[2023-06-28 18:27:11,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:11,352] [INFO] Task started: Prodigal
[2023-06-28 18:27:11,352] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1947bec-d5a6-4987-9c27-2d64ad0b1cc4/GCA_027404785.1_ASM2740478v1_genomic.fna.gz | prodigal -d GCA_027404785.1_ASM2740478v1_genomic.fna/cds.fna -a GCA_027404785.1_ASM2740478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:18,237] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:18,237] [INFO] Task started: HMMsearch
[2023-06-28 18:27:18,237] [INFO] Running command: hmmsearch --tblout GCA_027404785.1_ASM2740478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/reference_markers.hmm GCA_027404785.1_ASM2740478v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:18,460] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:18,461] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd1947bec-d5a6-4987-9c27-2d64ad0b1cc4/GCA_027404785.1_ASM2740478v1_genomic.fna.gz]
[2023-06-28 18:27:18,486] [INFO] Query marker FASTA was written to GCA_027404785.1_ASM2740478v1_genomic.fna/markers.fasta
[2023-06-28 18:27:18,486] [INFO] Task started: Blastn
[2023-06-28 18:27:18,486] [INFO] Running command: blastn -query GCA_027404785.1_ASM2740478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/reference_markers.fasta -out GCA_027404785.1_ASM2740478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:19,065] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:19,071] [INFO] Selected 15 target genomes.
[2023-06-28 18:27:19,071] [INFO] Target genome list was writen to GCA_027404785.1_ASM2740478v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:19,074] [INFO] Task started: fastANI
[2023-06-28 18:27:19,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1947bec-d5a6-4987-9c27-2d64ad0b1cc4/GCA_027404785.1_ASM2740478v1_genomic.fna.gz --refList GCA_027404785.1_ASM2740478v1_genomic.fna/target_genomes.txt --output GCA_027404785.1_ASM2740478v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:28,570] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:28,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:28,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:28,573] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:28,573] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 18:27:28,573] [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
--------------------------------------------------------------------------------
[2023-06-28 18:27:28,575] [INFO] DFAST Taxonomy check result was written to GCA_027404785.1_ASM2740478v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:28,576] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:28,577] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:28,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/checkm_data
[2023-06-28 18:27:28,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:28,614] [INFO] Task started: CheckM
[2023-06-28 18:27:28,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027404785.1_ASM2740478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027404785.1_ASM2740478v1_genomic.fna/checkm_input GCA_027404785.1_ASM2740478v1_genomic.fna/checkm_result
[2023-06-28 18:27:53,785] [INFO] Task succeeded: CheckM
[2023-06-28 18:27:53,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:27:53,808] [INFO] ===== Completeness check finished =====
[2023-06-28 18:27:53,808] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:27:53,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027404785.1_ASM2740478v1_genomic.fna/markers.fasta)
[2023-06-28 18:27:53,809] [INFO] Task started: Blastn
[2023-06-28 18:27:53,809] [INFO] Running command: blastn -query GCA_027404785.1_ASM2740478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5102467-4396-46b1-bb3f-a988bb15d3d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027404785.1_ASM2740478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:54,559] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:54,563] [INFO] Selected 10 target genomes.
[2023-06-28 18:27:54,563] [INFO] Target genome list was writen to GCA_027404785.1_ASM2740478v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:27:54,570] [INFO] Task started: fastANI
[2023-06-28 18:27:54,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1947bec-d5a6-4987-9c27-2d64ad0b1cc4/GCA_027404785.1_ASM2740478v1_genomic.fna.gz --refList GCA_027404785.1_ASM2740478v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027404785.1_ASM2740478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:00,657] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:00,672] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:28:00,673] [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_016208235.1	s__SURF-52 sp016208235	82.1847	328	793	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__SURF-52	95.0	98.97	98.97	0.86	0.86	2	-
GCA_003599195.1	s__SURF-52 sp003599195	80.8436	339	793	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_016875015.1	s__0-14-0-80-60-11 sp016875015	79.4623	210	793	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_018897875.1	s__0-14-0-80-60-11 sp018897875	78.8137	202	793	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__0-14-0-80-60-11	95.0	99.10	99.10	0.81	0.81	2	-
GCA_002779455.1	s__0-14-0-80-60-11 sp002779455	78.7758	161	793	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_016874915.1	s__0-14-0-80-60-11 sp016874915	78.507	200	793	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_016874945.1	s__0-14-0-80-60-11 sp016874945	78.4063	161	793	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_016874975.1	s__VGSQ01 sp016874975	78.1287	190	793	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__VGSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011358955.1	s__DTKJ01 sp011358955	77.6414	119	793	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__0-14-0-80-60-11;g__DTKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874895.1	s__Desulfobacca sp016874895	77.15	109	793	d__Bacteria;p__Desulfobacterota;c__Desulfobaccia;o__Desulfobaccales;f__Desulfobaccaceae;g__Desulfobacca	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:00,675] [INFO] GTDB search result was written to GCA_027404785.1_ASM2740478v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:00,676] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:00,679] [INFO] DFAST_QC result json was written to GCA_027404785.1_ASM2740478v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:00,680] [INFO] DFAST_QC completed!
[2023-06-28 18:28:00,680] [INFO] Total running time: 0h0m51s