[2023-03-15 06:28:21,433] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference
[2023-03-15 06:28:22,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,550] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,550] [INFO] Running command: cat /var/lib/cwl/stga49fc560-e5eb-4ef6-8886-d68f585ad214/OceanDNA-b24046.fa | prodigal -d OceanDNA-b24046/cds.fna -a OceanDNA-b24046/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:37,354] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:37,354] [INFO] Task started: HMMsearch
[2023-03-15 06:28:37,354] [INFO] Running command: hmmsearch --tblout OceanDNA-b24046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/reference_markers.hmm OceanDNA-b24046/protein.faa > /dev/null
[2023-03-15 06:28:37,539] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:37,539] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga49fc560-e5eb-4ef6-8886-d68f585ad214/OceanDNA-b24046.fa]
[2023-03-15 06:28:37,564] [INFO] Query marker FASTA was written to OceanDNA-b24046/markers.fasta
[2023-03-15 06:28:37,564] [INFO] Task started: Blastn
[2023-03-15 06:28:37,564] [INFO] Running command: blastn -query OceanDNA-b24046/markers.fasta -db /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/reference_markers.fasta -out OceanDNA-b24046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:38,162] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:38,163] [INFO] Selected 27 target genomes.
[2023-03-15 06:28:38,163] [INFO] Target genome list was writen to OceanDNA-b24046/target_genomes.txt
[2023-03-15 06:28:38,178] [INFO] Task started: fastANI
[2023-03-15 06:28:38,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga49fc560-e5eb-4ef6-8886-d68f585ad214/OceanDNA-b24046.fa --refList OceanDNA-b24046/target_genomes.txt --output OceanDNA-b24046/fastani_result.tsv --threads 1
[2023-03-15 06:28:59,940] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:59,941] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:59,941] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:59,952] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:59,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:28:59,953] [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
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.3167	60	736	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.117	82	736	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.0594	63	736	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.9352	85	736	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	75.9177	86	736	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.8007	53	736	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.7446	56	736	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7285	65	736	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.6522	66	736	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.6357	53	736	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	75.6264	58	736	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.5888	70	736	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.5084	83	736	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.5073	70	736	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	75.4549	55	736	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_002937075.1	333368	333368	type	True	75.3275	56	736	95	below_threshold
Rhodoblastus sphagnicola	strain=DSM 16996	GCA_014197735.1	333368	333368	type	True	75.2977	58	736	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	75.1274	67	736	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	75.1274	67	736	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.0889	79	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:28:59,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24046/tc_result.tsv
[2023-03-15 06:28:59,956] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:59,956] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:59,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/checkm_data
[2023-03-15 06:28:59,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:59,965] [INFO] Task started: CheckM
[2023-03-15 06:28:59,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24046/checkm_input OceanDNA-b24046/checkm_result
[2023-03-15 06:29:40,803] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:40,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.44%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:40,824] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:40,824] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:40,824] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24046/markers.fasta)
[2023-03-15 06:29:40,824] [INFO] Task started: Blastn
[2023-03-15 06:29:40,824] [INFO] Running command: blastn -query OceanDNA-b24046/markers.fasta -db /var/lib/cwl/stg8f464c09-ec16-414c-bb2f-59d07a050060/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:41,798] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:41,799] [INFO] Selected 28 target genomes.
[2023-03-15 06:29:41,799] [INFO] Target genome list was writen to OceanDNA-b24046/target_genomes_gtdb.txt
[2023-03-15 06:29:41,823] [INFO] Task started: fastANI
[2023-03-15 06:29:41,824] [INFO] Running command: fastANI --query /var/lib/cwl/stga49fc560-e5eb-4ef6-8886-d68f585ad214/OceanDNA-b24046.fa --refList OceanDNA-b24046/target_genomes_gtdb.txt --output OceanDNA-b24046/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:58,018] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:58,026] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:58,027] [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_009377375.1	s__WHUE01 sp009377375	76.5902	120	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.2975	60	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_006218045.1	s__Magnetospirillum sp006218045	76.194	51	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.1927	52	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.117	82	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.0664	51	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828515.1	s__CAIKMD01 sp903828515	75.9033	74	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__CAIKMD01	95.0	99.99	99.96	1.00	0.99	5	-
GCF_001511835.1	s__Phaeospirillum sp001511835	75.8632	51	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349665.1	s__Telmatospirillum sp013349665	75.8488	53	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	75.75	64	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240745.1	s__Reyranella sp018240745	75.4961	65	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937075.1	s__Rhodoblastus sphagnicola	75.3275	56	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_003226555.1	s__Rhodopseudomonas palustris_I	75.303	51	736	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:58,027] [INFO] GTDB search result was written to OceanDNA-b24046/result_gtdb.tsv
[2023-03-15 06:29:58,027] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:58,029] [INFO] DFAST_QC result json was written to OceanDNA-b24046/dqc_result.json
[2023-03-15 06:29:58,029] [INFO] DFAST_QC completed!
[2023-03-15 06:29:58,029] [INFO] Total running time: 0h1m37s