[2024-01-24 13:37:27,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference
[2024-01-24 13:37:28,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:28,892] [INFO] Task started: Prodigal
[2024-01-24 13:37:28,892] [INFO] Running command: gunzip -c /var/lib/cwl/stg67e9458e-8ecb-4474-8a39-7275f0076065/GCF_000350545.1_DPO2_genomic.fna.gz | prodigal -d GCF_000350545.1_DPO2_genomic.fna/cds.fna -a GCF_000350545.1_DPO2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:44,586] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:44,586] [INFO] Task started: HMMsearch
[2024-01-24 13:37:44,586] [INFO] Running command: hmmsearch --tblout GCF_000350545.1_DPO2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/reference_markers.hmm GCF_000350545.1_DPO2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:44,901] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:44,903] [INFO] Found 6/6 markers.
[2024-01-24 13:37:44,949] [INFO] Query marker FASTA was written to GCF_000350545.1_DPO2_genomic.fna/markers.fasta
[2024-01-24 13:37:44,949] [INFO] Task started: Blastn
[2024-01-24 13:37:44,949] [INFO] Running command: blastn -query GCF_000350545.1_DPO2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/reference_markers.fasta -out GCF_000350545.1_DPO2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:45,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:45,559] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:45,559] [INFO] Target genome list was writen to GCF_000350545.1_DPO2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:45,778] [INFO] Task started: fastANI
[2024-01-24 13:37:45,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e9458e-8ecb-4474-8a39-7275f0076065/GCF_000350545.1_DPO2_genomic.fna.gz --refList GCF_000350545.1_DPO2_genomic.fna/target_genomes.txt --output GCF_000350545.1_DPO2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:59,943] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:59,943] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:59,944] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:59,954] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:59,955] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:59,955] [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
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	100.0	1624	1645	95	inconclusive
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	96.8933	1298	1645	95	inconclusive
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.4836	347	1645	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	77.4241	147	1645	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	77.2324	175	1645	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	77.1515	195	1645	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	76.4858	173	1645	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.3076	107	1645	95	below_threshold
Desulfoluna spongiiphila	strain=AA1	GCA_900101345.1	419481	419481	type	True	76.2768	56	1645	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	76.035	78	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:59,957] [INFO] DFAST Taxonomy check result was written to GCF_000350545.1_DPO2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:59,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:59,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:59,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/checkm_data
[2024-01-24 13:37:59,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:00,011] [INFO] Task started: CheckM
[2024-01-24 13:38:00,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000350545.1_DPO2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000350545.1_DPO2_genomic.fna/checkm_input GCF_000350545.1_DPO2_genomic.fna/checkm_result
[2024-01-24 13:38:48,101] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:48,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:48,125] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:48,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:48,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000350545.1_DPO2_genomic.fna/markers.fasta)
[2024-01-24 13:38:48,126] [INFO] Task started: Blastn
[2024-01-24 13:38:48,126] [INFO] Running command: blastn -query GCF_000350545.1_DPO2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a685b6f-73e3-4616-8704-9ae807abf714/dqc_reference/reference_markers_gtdb.fasta -out GCF_000350545.1_DPO2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:48,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:48,933] [INFO] Selected 7 target genomes.
[2024-01-24 13:38:48,933] [INFO] Target genome list was writen to GCF_000350545.1_DPO2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:48,972] [INFO] Task started: fastANI
[2024-01-24 13:38:48,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg67e9458e-8ecb-4474-8a39-7275f0076065/GCF_000350545.1_DPO2_genomic.fna.gz --refList GCF_000350545.1_DPO2_genomic.fna/target_genomes_gtdb.txt --output GCF_000350545.1_DPO2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:55,857] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:55,871] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:38:55,871] [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
GCF_000350545.1	s__Desulfotignum phosphitoxidans	100.0	1622	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000421285.1	s__Desulfotignum balticum	96.8825	1298	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	inconclusive
GCA_018399285.1	s__Desulfotignum sp018399285	93.8567	895	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389555.1	s__Desulfotignum sp011389555	87.5191	814	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389835.1	s__Desulfotignum sp011389835	85.077	710	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390695.1	s__Desulfotignum sp011390695	81.6402	350	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389575.1	s__Desulfotignum sp011389575	80.8076	639	1645	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:55,873] [INFO] GTDB search result was written to GCF_000350545.1_DPO2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:55,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:55,878] [INFO] DFAST_QC result json was written to GCF_000350545.1_DPO2_genomic.fna/dqc_result.json
[2024-01-24 13:38:55,878] [INFO] DFAST_QC completed!
[2024-01-24 13:38:55,878] [INFO] Total running time: 0h1m28s