[2023-03-15 04:37:12,346] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:37:12,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:37:12,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference
[2023-03-15 04:37:13,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:37:13,451] [INFO] Task started: Prodigal
[2023-03-15 04:37:13,451] [INFO] Running command: cat /var/lib/cwl/stgcad9a2d7-21d6-4f46-9572-8ec33a6a3a3b/OceanDNA-b33230.fa | prodigal -d OceanDNA-b33230/cds.fna -a OceanDNA-b33230/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:37:22,119] [INFO] Task succeeded: Prodigal
[2023-03-15 04:37:22,119] [INFO] Task started: HMMsearch
[2023-03-15 04:37:22,119] [INFO] Running command: hmmsearch --tblout OceanDNA-b33230/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/reference_markers.hmm OceanDNA-b33230/protein.faa > /dev/null
[2023-03-15 04:37:22,300] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:37:22,300] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcad9a2d7-21d6-4f46-9572-8ec33a6a3a3b/OceanDNA-b33230.fa]
[2023-03-15 04:37:22,316] [INFO] Query marker FASTA was written to OceanDNA-b33230/markers.fasta
[2023-03-15 04:37:22,317] [INFO] Task started: Blastn
[2023-03-15 04:37:22,318] [INFO] Running command: blastn -query OceanDNA-b33230/markers.fasta -db /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/reference_markers.fasta -out OceanDNA-b33230/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:37:23,018] [INFO] Task succeeded: Blastn
[2023-03-15 04:37:23,023] [INFO] Selected 26 target genomes.
[2023-03-15 04:37:23,023] [INFO] Target genome list was writen to OceanDNA-b33230/target_genomes.txt
[2023-03-15 04:37:23,038] [INFO] Task started: fastANI
[2023-03-15 04:37:23,038] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad9a2d7-21d6-4f46-9572-8ec33a6a3a3b/OceanDNA-b33230.fa --refList OceanDNA-b33230/target_genomes.txt --output OceanDNA-b33230/fastani_result.tsv --threads 1
[2023-03-15 04:37:41,396] [INFO] Task succeeded: fastANI
[2023-03-15 04:37:41,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:37:41,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:37:41,403] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:37:41,403] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:37:41,403] [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
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.5868	55	443	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.3652	70	443	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.1569	55	443	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0618	57	443	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	76.0141	62	443	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	75.7353	59	443	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	75.7256	51	443	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.7006	51	443	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.5424	69	443	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:37:41,406] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33230/tc_result.tsv
[2023-03-15 04:37:41,408] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:37:41,408] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:37:41,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/checkm_data
[2023-03-15 04:37:41,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:37:41,414] [INFO] Task started: CheckM
[2023-03-15 04:37:41,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33230/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33230/checkm_input OceanDNA-b33230/checkm_result
[2023-03-15 04:38:07,669] [INFO] Task succeeded: CheckM
[2023-03-15 04:38:07,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:38:07,709] [INFO] ===== Completeness check finished =====
[2023-03-15 04:38:07,709] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:38:07,710] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33230/markers.fasta)
[2023-03-15 04:38:07,710] [INFO] Task started: Blastn
[2023-03-15 04:38:07,710] [INFO] Running command: blastn -query OceanDNA-b33230/markers.fasta -db /var/lib/cwl/stg35820b3a-258f-42f3-828c-0050288d0d04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33230/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:38:08,837] [INFO] Task succeeded: Blastn
[2023-03-15 04:38:08,842] [INFO] Selected 27 target genomes.
[2023-03-15 04:38:08,843] [INFO] Target genome list was writen to OceanDNA-b33230/target_genomes_gtdb.txt
[2023-03-15 04:38:08,872] [INFO] Task started: fastANI
[2023-03-15 04:38:08,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad9a2d7-21d6-4f46-9572-8ec33a6a3a3b/OceanDNA-b33230.fa --refList OceanDNA-b33230/target_genomes_gtdb.txt --output OceanDNA-b33230/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:38:23,464] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:23,472] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:38:23,472] [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_014762505.1	s__SpSt-1174 sp014762505	76.7417	57	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	76.5679	58	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	76.5261	62	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	76.2863	71	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584105.1	s__Ectothiorhodospira shaposhnikovii	76.2653	55	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.2604	53	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.1559	55	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.1336	57	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.1277	56	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583825.1	s__Thiohalocapsa halophila	75.9887	63	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	95.31	95.31	0.87	0.87	2	-
GCF_000633935.1	s__Ectothiorhodospira haloalkaliphila	75.8276	51	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	99.86	99.86	0.97	0.97	2	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	75.6884	53	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:38:23,475] [INFO] GTDB search result was written to OceanDNA-b33230/result_gtdb.tsv
[2023-03-15 04:38:23,477] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:38:23,482] [INFO] DFAST_QC result json was written to OceanDNA-b33230/dqc_result.json
[2023-03-15 04:38:23,482] [INFO] DFAST_QC completed!
[2023-03-15 04:38:23,482] [INFO] Total running time: 0h1m11s