[2023-03-14 11:49:17,041] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:17,044] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:17,044] [INFO] DQC Reference Directory: /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference
[2023-03-14 11:49:18,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:18,142] [INFO] Task started: Prodigal
[2023-03-14 11:49:18,142] [INFO] Running command: cat /var/lib/cwl/stgd038c0a0-5c4e-4512-b0e5-e9e8606590af/OceanDNA-b17085.fa | prodigal -d OceanDNA-b17085/cds.fna -a OceanDNA-b17085/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:50,843] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:50,843] [INFO] Task started: HMMsearch
[2023-03-14 11:49:50,843] [INFO] Running command: hmmsearch --tblout OceanDNA-b17085/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/reference_markers.hmm OceanDNA-b17085/protein.faa > /dev/null
[2023-03-14 11:49:51,139] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:51,139] [INFO] Found 6/6 markers.
[2023-03-14 11:49:51,185] [INFO] Query marker FASTA was written to OceanDNA-b17085/markers.fasta
[2023-03-14 11:49:51,186] [INFO] Task started: Blastn
[2023-03-14 11:49:51,187] [INFO] Running command: blastn -query OceanDNA-b17085/markers.fasta -db /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/reference_markers.fasta -out OceanDNA-b17085/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:51,739] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:51,744] [INFO] Selected 19 target genomes.
[2023-03-14 11:49:51,745] [INFO] Target genome list was writen to OceanDNA-b17085/target_genomes.txt
[2023-03-14 11:49:51,757] [INFO] Task started: fastANI
[2023-03-14 11:49:51,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgd038c0a0-5c4e-4512-b0e5-e9e8606590af/OceanDNA-b17085.fa --refList OceanDNA-b17085/target_genomes.txt --output OceanDNA-b17085/fastani_result.tsv --threads 1
[2023-03-14 11:50:05,756] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:05,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:50:05,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:50:05,763] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:50:05,764] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:50:05,764] [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
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.549	381	1730	95	below_threshold
Desulfobacter postgatei	strain=2ac9	GCA_000233695.3	2293	2293	type	True	77.3528	151	1730	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	77.148	219	1730	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	77.0835	168	1730	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	76.8668	181	1730	95	below_threshold
Desulfobacter hydrogenophilus	strain=AcRS1	GCA_004319545.1	2291	2291	type	True	76.8652	184	1730	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	76.8476	190	1730	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_003261095.1	2291	2291	type	True	76.8379	186	1730	95	below_threshold
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	76.6605	258	1730	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	76.6437	249	1730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:50:05,766] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17085/tc_result.tsv
[2023-03-14 11:50:05,771] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:50:05,772] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:50:05,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/checkm_data
[2023-03-14 11:50:05,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:50:05,783] [INFO] Task started: CheckM
[2023-03-14 11:50:05,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17085/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17085/checkm_input OceanDNA-b17085/checkm_result
[2023-03-14 11:51:25,255] [INFO] Task succeeded: CheckM
[2023-03-14 11:51:25,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:51:25,342] [INFO] ===== Completeness check finished =====
[2023-03-14 11:51:25,342] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:51:25,343] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17085/markers.fasta)
[2023-03-14 11:51:25,344] [INFO] Task started: Blastn
[2023-03-14 11:51:25,344] [INFO] Running command: blastn -query OceanDNA-b17085/markers.fasta -db /var/lib/cwl/stgd09c2994-1e1e-447e-aae3-2e658a3d5309/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17085/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:51:26,113] [INFO] Task succeeded: Blastn
[2023-03-14 11:51:26,121] [INFO] Selected 18 target genomes.
[2023-03-14 11:51:26,121] [INFO] Target genome list was writen to OceanDNA-b17085/target_genomes_gtdb.txt
[2023-03-14 11:51:26,266] [INFO] Task started: fastANI
[2023-03-14 11:51:26,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgd038c0a0-5c4e-4512-b0e5-e9e8606590af/OceanDNA-b17085.fa --refList OceanDNA-b17085/target_genomes_gtdb.txt --output OceanDNA-b17085/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:51:38,286] [INFO] Task succeeded: fastANI
[2023-03-14 11:51:38,295] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:51:38,295] [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_003538835.1	s__Desulfobacter sp003538835	99.7448	1440	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003252055.1	s__Desulfobacter postgatei_B	77.5928	131	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000233695.2	s__Desulfobacter postgatei	77.3722	150	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	96.23	96.02	0.82	0.77	7	-
GCF_000745975.1	s__Desulfobacter vibrioformis	77.148	219	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013389365.1	s__Desulfobacter latus	77.0835	168	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013792075.1	s__NBML01 sp013792075	77.0444	274	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	99.85	99.75	0.95	0.94	3	-
GCF_004319545.1	s__Desulfobacter hydrogenophilus	76.8915	181	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000373985.1	s__Desulfobacter curvatus	76.8603	189	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816605.1	s__NBML01 sp018816605	76.8301	248	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004796375.1	s__MADRE2 sp004796375	76.8164	173	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__MADRE2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390615.1	s__Desulfotignum sp011390615	76.8026	212	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747145.1	s__Desulfobacter postgatei_A	76.7876	91	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031875.1	s__Desulfobacula sp012031875	76.761	221	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389715.1	s__Desulfotignum sp011389715	76.6843	164	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002085465.1	s__NBML01 sp002085465	76.3652	65	1730	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__NBML01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:51:38,300] [INFO] GTDB search result was written to OceanDNA-b17085/result_gtdb.tsv
[2023-03-14 11:51:38,306] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:51:38,311] [INFO] DFAST_QC result json was written to OceanDNA-b17085/dqc_result.json
[2023-03-14 11:51:38,311] [INFO] DFAST_QC completed!
[2023-03-14 11:51:38,311] [INFO] Total running time: 0h2m21s