[2023-03-15 16:28:44,764] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:28:44,764] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:28:44,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference
[2023-03-15 16:28:45,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:28:45,888] [INFO] Task started: Prodigal
[2023-03-15 16:28:45,888] [INFO] Running command: cat /var/lib/cwl/stge1b10748-5097-424f-8f99-c77413283188/OceanDNA-b6723.fa | prodigal -d OceanDNA-b6723/cds.fna -a OceanDNA-b6723/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:29:04,410] [INFO] Task succeeded: Prodigal
[2023-03-15 16:29:04,410] [INFO] Task started: HMMsearch
[2023-03-15 16:29:04,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b6723/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/reference_markers.hmm OceanDNA-b6723/protein.faa > /dev/null
[2023-03-15 16:29:04,615] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:29:04,615] [INFO] Found 6/6 markers.
[2023-03-15 16:29:04,646] [INFO] Query marker FASTA was written to OceanDNA-b6723/markers.fasta
[2023-03-15 16:29:04,647] [INFO] Task started: Blastn
[2023-03-15 16:29:04,647] [INFO] Running command: blastn -query OceanDNA-b6723/markers.fasta -db /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/reference_markers.fasta -out OceanDNA-b6723/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:29:05,229] [INFO] Task succeeded: Blastn
[2023-03-15 16:29:05,235] [INFO] Selected 34 target genomes.
[2023-03-15 16:29:05,235] [INFO] Target genome list was writen to OceanDNA-b6723/target_genomes.txt
[2023-03-15 16:29:05,255] [INFO] Task started: fastANI
[2023-03-15 16:29:05,255] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b10748-5097-424f-8f99-c77413283188/OceanDNA-b6723.fa --refList OceanDNA-b6723/target_genomes.txt --output OceanDNA-b6723/fastani_result.tsv --threads 1
[2023-03-15 16:29:28,811] [INFO] Task succeeded: fastANI
[2023-03-15 16:29:28,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:29:28,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:29:28,822] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:29:28,822] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:29:28,822] [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
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	76.3742	67	738	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	76.2218	90	738	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.2011	105	738	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	76.0969	66	738	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.0773	61	738	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.0371	97	738	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.0252	78	738	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.0047	86	738	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	75.692	55	738	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.688	86	738	95	below_threshold
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	75.6339	51	738	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	75.544	74	738	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	75.544	74	738	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	75.5062	56	738	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	75.4818	56	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:29:28,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6723/tc_result.tsv
[2023-03-15 16:29:28,822] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:29:28,823] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:29:28,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/checkm_data
[2023-03-15 16:29:28,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:29:28,829] [INFO] Task started: CheckM
[2023-03-15 16:29:28,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6723/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6723/checkm_input OceanDNA-b6723/checkm_result
[2023-03-15 16:30:18,771] [INFO] Task succeeded: CheckM
[2023-03-15 16:30:18,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:30:18,775] [INFO] ===== Completeness check finished =====
[2023-03-15 16:30:18,775] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:30:18,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6723/markers.fasta)
[2023-03-15 16:30:18,776] [INFO] Task started: Blastn
[2023-03-15 16:30:18,776] [INFO] Running command: blastn -query OceanDNA-b6723/markers.fasta -db /var/lib/cwl/stg5e2b49db-a3fa-44be-b994-36bcac6ebaf0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6723/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:30:19,683] [INFO] Task succeeded: Blastn
[2023-03-15 16:30:19,685] [INFO] Selected 33 target genomes.
[2023-03-15 16:30:19,685] [INFO] Target genome list was writen to OceanDNA-b6723/target_genomes_gtdb.txt
[2023-03-15 16:30:19,755] [INFO] Task started: fastANI
[2023-03-15 16:30:19,755] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b10748-5097-424f-8f99-c77413283188/OceanDNA-b6723.fa --refList OceanDNA-b6723/target_genomes_gtdb.txt --output OceanDNA-b6723/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:30:41,839] [INFO] Task succeeded: fastANI
[2023-03-15 16:30:41,850] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:30:41,851] [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_009797885.1	s__Croceivirga sp009797885	76.9545	197	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	76.369	89	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	76.3376	85	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.2687	84	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	76.2247	90	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	76.2011	105	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795065.1	s__Muricauda sp017795065	76.1644	74	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	76.1094	65	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	76.0773	61	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	76.0508	85	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.0371	97	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.0252	78	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_005937185.1	s__Muricauda algicola	76.0047	86	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	75.9778	73	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269385.1	s__Maribacter cobaltidurans	75.9253	53	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000745185.1	s__Muricauda sp000745185	75.8024	94	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885635.1	s__RZ26 sp005885635	75.692	55	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	75.688	86	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330165.1	s__Zobellia sp015330165	75.6339	51	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_014235875.1	s__Croceivirga lutea	75.544	74	738	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:30:41,852] [INFO] GTDB search result was written to OceanDNA-b6723/result_gtdb.tsv
[2023-03-15 16:30:41,852] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:30:41,855] [INFO] DFAST_QC result json was written to OceanDNA-b6723/dqc_result.json
[2023-03-15 16:30:41,855] [INFO] DFAST_QC completed!
[2023-03-15 16:30:41,855] [INFO] Total running time: 0h1m57s