[2023-06-16 19:32:18,056] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:32:18,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:32:18,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference
[2023-06-16 19:32:19,301] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:32:19,302] [INFO] Task started: Prodigal
[2023-06-16 19:32:19,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f4576a7-1af6-4fb9-a538-24bd7902460d/GCA_905176665.1_D4_OalgB6SA_genomic.fna.gz | prodigal -d GCA_905176665.1_D4_OalgB6SA_genomic.fna/cds.fna -a GCA_905176665.1_D4_OalgB6SA_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:32:34,739] [INFO] Task succeeded: Prodigal
[2023-06-16 19:32:34,740] [INFO] Task started: HMMsearch
[2023-06-16 19:32:34,740] [INFO] Running command: hmmsearch --tblout GCA_905176665.1_D4_OalgB6SA_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/reference_markers.hmm GCA_905176665.1_D4_OalgB6SA_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:32:35,071] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:32:35,073] [INFO] Found 6/6 markers.
[2023-06-16 19:32:35,121] [INFO] Query marker FASTA was written to GCA_905176665.1_D4_OalgB6SA_genomic.fna/markers.fasta
[2023-06-16 19:32:35,122] [INFO] Task started: Blastn
[2023-06-16 19:32:35,122] [INFO] Running command: blastn -query GCA_905176665.1_D4_OalgB6SA_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/reference_markers.fasta -out GCA_905176665.1_D4_OalgB6SA_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:32:35,733] [INFO] Task succeeded: Blastn
[2023-06-16 19:32:35,740] [INFO] Selected 24 target genomes.
[2023-06-16 19:32:35,740] [INFO] Target genome list was writen to GCA_905176665.1_D4_OalgB6SA_genomic.fna/target_genomes.txt
[2023-06-16 19:32:35,744] [INFO] Task started: fastANI
[2023-06-16 19:32:35,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4576a7-1af6-4fb9-a538-24bd7902460d/GCA_905176665.1_D4_OalgB6SA_genomic.fna.gz --refList GCA_905176665.1_D4_OalgB6SA_genomic.fna/target_genomes.txt --output GCA_905176665.1_D4_OalgB6SA_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:32:52,303] [INFO] Task succeeded: fastANI
[2023-06-16 19:32:52,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:32:52,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:32:52,319] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:32:52,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:32:52,320] [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
Desulfococcus multivorans	strain=DSM 2059	GCA_002009335.2	897	897	type	True	76.5251	69	1761	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_900167235.1	897	897	type	True	76.5068	69	1761	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_000422185.1	897	897	type	True	76.47	68	1761	95	below_threshold
Desulfococcus multivorans	strain=DSM 2059	GCA_001854245.1	897	897	type	True	76.4436	69	1761	95	below_threshold
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	76.2628	109	1761	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.0633	123	1761	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.0481	131	1761	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	75.9782	111	1761	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:32:52,322] [INFO] DFAST Taxonomy check result was written to GCA_905176665.1_D4_OalgB6SA_genomic.fna/tc_result.tsv
[2023-06-16 19:32:52,323] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:32:52,323] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:32:52,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/checkm_data
[2023-06-16 19:32:52,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:32:52,388] [INFO] Task started: CheckM
[2023-06-16 19:32:52,388] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905176665.1_D4_OalgB6SA_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905176665.1_D4_OalgB6SA_genomic.fna/checkm_input GCA_905176665.1_D4_OalgB6SA_genomic.fna/checkm_result
[2023-06-16 19:33:39,514] [INFO] Task succeeded: CheckM
[2023-06-16 19:33:39,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:33:39,537] [INFO] ===== Completeness check finished =====
[2023-06-16 19:33:39,538] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:33:39,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905176665.1_D4_OalgB6SA_genomic.fna/markers.fasta)
[2023-06-16 19:33:39,539] [INFO] Task started: Blastn
[2023-06-16 19:33:39,539] [INFO] Running command: blastn -query GCA_905176665.1_D4_OalgB6SA_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e38e5d5-7de7-4ea8-946e-4440eb0ae7e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_905176665.1_D4_OalgB6SA_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:33:40,344] [INFO] Task succeeded: Blastn
[2023-06-16 19:33:40,349] [INFO] Selected 23 target genomes.
[2023-06-16 19:33:40,349] [INFO] Target genome list was writen to GCA_905176665.1_D4_OalgB6SA_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:33:40,358] [INFO] Task started: fastANI
[2023-06-16 19:33:40,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f4576a7-1af6-4fb9-a538-24bd7902460d/GCA_905176665.1_D4_OalgB6SA_genomic.fna.gz --refList GCA_905176665.1_D4_OalgB6SA_genomic.fna/target_genomes_gtdb.txt --output GCA_905176665.1_D4_OalgB6SA_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:33:59,119] [INFO] Task succeeded: fastANI
[2023-06-16 19:33:59,131] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:33:59,132] [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_905176665.1	s__CAJINA01 sp905176665	100.0	1755	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__CAJINA01;g__CAJINA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001854245.1	s__Desulfococcus multivorans	76.7151	71	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfococcus	95.0	100.00	99.99	1.00	1.00	4	-
GCA_011042305.1	s__UBA2174 sp011042305	76.1915	91	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009689005.1	s__Desulfosarcina ovata	76.0375	132	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	97.03	97.03	0.77	0.77	2	-
GCA_016342285.1	s__JAEINQ01 sp016342285	76.0326	155	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001303025.1	s__SG8-13 sp001303025	76.0234	74	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SG8-13;g__SG8-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	76.0145	94	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016735415.1	s__JABZFP01 sp016735415	75.982	75	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__JABZFP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311845.1	s__Desulfosarcina cetonica	75.9782	111	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.91	99.91	0.98	0.98	2	-
GCA_011390065.1	s__JAABTD01 sp011390065	75.907	94	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390345.1	s__JAABSP01 sp011390345	75.8637	70	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSP01	95.0	95.08	95.08	0.82	0.82	2	-
GCA_003599575.1	s__Desulfatitalea sp003599575	75.7281	77	1761	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:33:59,134] [INFO] GTDB search result was written to GCA_905176665.1_D4_OalgB6SA_genomic.fna/result_gtdb.tsv
[2023-06-16 19:33:59,135] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:33:59,149] [INFO] DFAST_QC result json was written to GCA_905176665.1_D4_OalgB6SA_genomic.fna/dqc_result.json
[2023-06-16 19:33:59,150] [INFO] DFAST_QC completed!
[2023-06-16 19:33:59,150] [INFO] Total running time: 0h1m41s