[2023-03-17 11:38:03,744] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:38:03,744] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:38:03,744] [INFO] DQC Reference Directory: /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference
[2023-03-17 11:38:04,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:38:04,857] [INFO] Task started: Prodigal
[2023-03-17 11:38:04,857] [INFO] Running command: cat /var/lib/cwl/stg67766428-3dd7-4ec3-86e7-c492d22cdb11/OceanDNA-b939.fa | prodigal -d OceanDNA-b939/cds.fna -a OceanDNA-b939/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:38:15,416] [INFO] Task succeeded: Prodigal
[2023-03-17 11:38:15,416] [INFO] Task started: HMMsearch
[2023-03-17 11:38:15,417] [INFO] Running command: hmmsearch --tblout OceanDNA-b939/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/reference_markers.hmm OceanDNA-b939/protein.faa > /dev/null
[2023-03-17 11:38:15,583] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:38:15,583] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg67766428-3dd7-4ec3-86e7-c492d22cdb11/OceanDNA-b939.fa]
[2023-03-17 11:38:15,602] [INFO] Query marker FASTA was written to OceanDNA-b939/markers.fasta
[2023-03-17 11:38:15,602] [INFO] Task started: Blastn
[2023-03-17 11:38:15,602] [INFO] Running command: blastn -query OceanDNA-b939/markers.fasta -db /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/reference_markers.fasta -out OceanDNA-b939/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:16,149] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:16,151] [INFO] Selected 29 target genomes.
[2023-03-17 11:38:16,151] [INFO] Target genome list was writen to OceanDNA-b939/target_genomes.txt
[2023-03-17 11:38:16,171] [INFO] Task started: fastANI
[2023-03-17 11:38:16,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg67766428-3dd7-4ec3-86e7-c492d22cdb11/OceanDNA-b939.fa --refList OceanDNA-b939/target_genomes.txt --output OceanDNA-b939/fastani_result.tsv --threads 1
[2023-03-17 11:38:38,231] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:38,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:38:38,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:38:38,241] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:38:38,241] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:38:38,241] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.3625	168	566	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.063	173	566	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.726	121	566	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3054	125	566	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	75.6637	85	566	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	75.6431	51	566	95	below_threshold
Streptomyces boncukensis	strain=SB3404	GCA_011045075.1	2711219	2711219	type	True	75.6276	69	566	95	below_threshold
Propioniciclava coleopterorum	strain=HDW11	GCA_011393335.1	2714937	2714937	type	True	75.6168	58	566	95	below_threshold
Promicromonospora soli	strain=CGMCC 4.7398	GCA_014653785.1	2035533	2035533	type	True	75.5042	56	566	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	75.4218	92	566	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	75.4038	83	566	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.3088	98	566	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	75.2899	115	566	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	75.1661	115	566	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:38:38,243] [INFO] DFAST Taxonomy check result was written to OceanDNA-b939/tc_result.tsv
[2023-03-17 11:38:38,243] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:38:38,243] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:38:38,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/checkm_data
[2023-03-17 11:38:38,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:38:38,253] [INFO] Task started: CheckM
[2023-03-17 11:38:38,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b939/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b939/checkm_input OceanDNA-b939/checkm_result
[2023-03-17 11:39:08,213] [INFO] Task succeeded: CheckM
[2023-03-17 11:39:08,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:39:08,269] [INFO] ===== Completeness check finished =====
[2023-03-17 11:39:08,269] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:39:08,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b939/markers.fasta)
[2023-03-17 11:39:08,270] [INFO] Task started: Blastn
[2023-03-17 11:39:08,270] [INFO] Running command: blastn -query OceanDNA-b939/markers.fasta -db /var/lib/cwl/stg894224f6-9951-4ce2-8414-45e4cb0d2262/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b939/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:39:09,064] [INFO] Task succeeded: Blastn
[2023-03-17 11:39:09,067] [INFO] Selected 8 target genomes.
[2023-03-17 11:39:09,067] [INFO] Target genome list was writen to OceanDNA-b939/target_genomes_gtdb.txt
[2023-03-17 11:39:09,074] [INFO] Task started: fastANI
[2023-03-17 11:39:09,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg67766428-3dd7-4ec3-86e7-c492d22cdb11/OceanDNA-b939.fa --refList OceanDNA-b939/target_genomes_gtdb.txt --output OceanDNA-b939/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:39:12,839] [INFO] Task succeeded: fastANI
[2023-03-17 11:39:12,845] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:39:12,845] [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_002699725.1	s__S20-B6 sp002699725	91.7205	470	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_002329075.1	s__S20-B6 sp002329075	87.7023	478	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
GCA_014381945.1	s__S20-B6 sp014381945	86.5412	497	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002346745.1	s__S20-B6 sp002346745	83.2109	405	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_016845305.1	s__UBA9410 sp016845305	80.2015	349	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	79.0968	283	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002255565.1	s__RAAP-2 sp002255565	76.4783	60	566	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	75.6219	52	566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:39:12,847] [INFO] GTDB search result was written to OceanDNA-b939/result_gtdb.tsv
[2023-03-17 11:39:12,850] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:39:12,854] [INFO] DFAST_QC result json was written to OceanDNA-b939/dqc_result.json
[2023-03-17 11:39:12,854] [INFO] DFAST_QC completed!
[2023-03-17 11:39:12,854] [INFO] Total running time: 0h1m9s