[2023-06-13 18:55:46,982] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:55:47,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:55:47,014] [INFO] DQC Reference Directory: /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference
[2023-06-13 18:55:48,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:55:48,103] [INFO] Task started: Prodigal
[2023-06-13 18:55:48,103] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be5d428-fcdd-41f0-b1e1-0f10e12cd025/GCA_022340405.1_ASM2234040v1_genomic.fna.gz | prodigal -d GCA_022340405.1_ASM2234040v1_genomic.fna/cds.fna -a GCA_022340405.1_ASM2234040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:55:57,786] [INFO] Task succeeded: Prodigal
[2023-06-13 18:55:57,786] [INFO] Task started: HMMsearch
[2023-06-13 18:55:57,786] [INFO] Running command: hmmsearch --tblout GCA_022340405.1_ASM2234040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/reference_markers.hmm GCA_022340405.1_ASM2234040v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:55:58,047] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:55:58,048] [INFO] Found 6/6 markers.
[2023-06-13 18:55:58,080] [INFO] Query marker FASTA was written to GCA_022340405.1_ASM2234040v1_genomic.fna/markers.fasta
[2023-06-13 18:55:58,081] [INFO] Task started: Blastn
[2023-06-13 18:55:58,081] [INFO] Running command: blastn -query GCA_022340405.1_ASM2234040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/reference_markers.fasta -out GCA_022340405.1_ASM2234040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:55:58,657] [INFO] Task succeeded: Blastn
[2023-06-13 18:55:58,660] [INFO] Selected 23 target genomes.
[2023-06-13 18:55:58,660] [INFO] Target genome list was writen to GCA_022340405.1_ASM2234040v1_genomic.fna/target_genomes.txt
[2023-06-13 18:55:58,663] [INFO] Task started: fastANI
[2023-06-13 18:55:58,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be5d428-fcdd-41f0-b1e1-0f10e12cd025/GCA_022340405.1_ASM2234040v1_genomic.fna.gz --refList GCA_022340405.1_ASM2234040v1_genomic.fna/target_genomes.txt --output GCA_022340405.1_ASM2234040v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:56:15,754] [INFO] Task succeeded: fastANI
[2023-06-13 18:56:15,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:56:15,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:56:15,763] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:56:15,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:56:15,763] [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
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.775	143	1165	95	below_threshold
Desulfatitalea tepidiphila	strain=S28bF	GCA_001293685.1	1185843	1185843	type	True	76.556	94	1165	95	below_threshold
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	76.4415	136	1165	95	below_threshold
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	76.2764	61	1165	95	below_threshold
Desulfatibacillum alkenivorans	strain=DSM 16219	GCA_900142135.1	259354	259354	type	True	76.1983	54	1165	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.1955	103	1165	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.1184	104	1165	95	below_threshold
Desulfosarcina cetonica	strain=JCM 12296	GCA_001311845.1	90730	90730	type	True	75.9991	110	1165	95	below_threshold
Desulfatirhabdium butyrativorans	strain=DSM 18734	GCA_000429925.1	340467	340467	type	True	75.8982	53	1165	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:56:15,765] [INFO] DFAST Taxonomy check result was written to GCA_022340405.1_ASM2234040v1_genomic.fna/tc_result.tsv
[2023-06-13 18:56:15,765] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:56:15,765] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:56:15,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/checkm_data
[2023-06-13 18:56:15,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:56:15,806] [INFO] Task started: CheckM
[2023-06-13 18:56:15,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022340405.1_ASM2234040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022340405.1_ASM2234040v1_genomic.fna/checkm_input GCA_022340405.1_ASM2234040v1_genomic.fna/checkm_result
[2023-06-13 18:56:45,878] [INFO] Task succeeded: CheckM
[2023-06-13 18:56:45,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:56:45,898] [INFO] ===== Completeness check finished =====
[2023-06-13 18:56:45,898] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:56:45,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022340405.1_ASM2234040v1_genomic.fna/markers.fasta)
[2023-06-13 18:56:45,900] [INFO] Task started: Blastn
[2023-06-13 18:56:45,900] [INFO] Running command: blastn -query GCA_022340405.1_ASM2234040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf027ea7e-0263-4a2e-bc91-c495de73323a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022340405.1_ASM2234040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:56:46,691] [INFO] Task succeeded: Blastn
[2023-06-13 18:56:46,694] [INFO] Selected 29 target genomes.
[2023-06-13 18:56:46,694] [INFO] Target genome list was writen to GCA_022340405.1_ASM2234040v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:56:46,723] [INFO] Task started: fastANI
[2023-06-13 18:56:46,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be5d428-fcdd-41f0-b1e1-0f10e12cd025/GCA_022340405.1_ASM2234040v1_genomic.fna.gz --refList GCA_022340405.1_ASM2234040v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022340405.1_ASM2234040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:57:05,664] [INFO] Task succeeded: fastANI
[2023-06-13 18:57:05,673] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:57:05,673] [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_002327445.1	s__UBA2174 sp002327445	76.9108	110	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	99.95	99.95	0.95	0.95	2	-
GCA_011390985.1	s__JAABRJ01 sp011390985	76.8163	72	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAABRJ01;g__JAABRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	76.8058	141	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	76.7839	132	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011042305.1	s__UBA2174 sp011042305	76.6978	118	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA2174;g__UBA2174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001293685.1	s__Desulfatitalea tepidiphila	76.5791	93	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432195.1	s__UBA5852 sp002432195	76.5259	126	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__UBA5852;g__UBA5852	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342285.1	s__JAEINQ01 sp016342285	76.5079	100	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688945.1	s__Desulfosarcina alkanivorans	76.4415	136	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390065.1	s__JAABTD01 sp011390065	76.3415	124	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599575.1	s__Desulfatitalea sp003599575	76.2825	69	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018405.1	s__Desulfosudis oleovorans	76.2764	61	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961655.1	s__Desulfatitalea sp000961655	76.1895	64	1165	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:57:05,675] [INFO] GTDB search result was written to GCA_022340405.1_ASM2234040v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:57:05,675] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:57:05,678] [INFO] DFAST_QC result json was written to GCA_022340405.1_ASM2234040v1_genomic.fna/dqc_result.json
[2023-06-13 18:57:05,678] [INFO] DFAST_QC completed!
[2023-06-13 18:57:05,678] [INFO] Total running time: 0h1m19s