[2023-03-14 12:29:45,259] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:29:45,259] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:29:45,259] [INFO] DQC Reference Directory: /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference
[2023-03-14 12:29:46,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:29:46,367] [INFO] Task started: Prodigal
[2023-03-14 12:29:46,368] [INFO] Running command: cat /var/lib/cwl/stgab2a0a51-3924-4dcc-b53a-13f687cad694/OceanDNA-b24959.fa | prodigal -d OceanDNA-b24959/cds.fna -a OceanDNA-b24959/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:30:08,255] [INFO] Task succeeded: Prodigal
[2023-03-14 12:30:08,255] [INFO] Task started: HMMsearch
[2023-03-14 12:30:08,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b24959/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/reference_markers.hmm OceanDNA-b24959/protein.faa > /dev/null
[2023-03-14 12:30:08,472] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:30:08,473] [INFO] Found 6/6 markers.
[2023-03-14 12:30:08,494] [INFO] Query marker FASTA was written to OceanDNA-b24959/markers.fasta
[2023-03-14 12:30:08,495] [INFO] Task started: Blastn
[2023-03-14 12:30:08,495] [INFO] Running command: blastn -query OceanDNA-b24959/markers.fasta -db /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/reference_markers.fasta -out OceanDNA-b24959/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:30:09,367] [INFO] Task succeeded: Blastn
[2023-03-14 12:30:09,368] [INFO] Selected 23 target genomes.
[2023-03-14 12:30:09,368] [INFO] Target genome list was writen to OceanDNA-b24959/target_genomes.txt
[2023-03-14 12:30:09,375] [INFO] Task started: fastANI
[2023-03-14 12:30:09,375] [INFO] Running command: fastANI --query /var/lib/cwl/stgab2a0a51-3924-4dcc-b53a-13f687cad694/OceanDNA-b24959.fa --refList OceanDNA-b24959/target_genomes.txt --output OceanDNA-b24959/fastani_result.tsv --threads 1
[2023-03-14 12:30:26,999] [INFO] Task succeeded: fastANI
[2023-03-14 12:30:26,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:30:26,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:30:27,012] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:30:27,012] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:30:27,012] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	81.9521	776	1177	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	79.5165	580	1177	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	79.1097	520	1177	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.4002	311	1177	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.805	177	1177	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.7451	181	1177	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.6537	216	1177	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.58	192	1177	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	76.5771	135	1177	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.5613	165	1177	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.4922	124	1177	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	76.3973	181	1177	95	below_threshold
Bradyrhizobium agreste	strain=CNPSo 4010	GCA_016031625.1	2751811	2751811	type	True	76.3515	159	1177	95	below_threshold
Bradyrhizobium sacchari	strain=p9-20	GCA_002068095.1	1399419	1399419	type	True	76.3509	162	1177	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	76.3393	132	1177	95	below_threshold
Stappia taiwanensis	strain=DSM 23284	GCA_013868145.1	992267	992267	type	True	76.3051	132	1177	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.2776	134	1177	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	76.2437	155	1177	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	76.1564	59	1177	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.9599	172	1177	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.5589	92	1177	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.3823	93	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:30:27,015] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24959/tc_result.tsv
[2023-03-14 12:30:27,017] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:30:27,017] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:30:27,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/checkm_data
[2023-03-14 12:30:27,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:30:27,026] [INFO] Task started: CheckM
[2023-03-14 12:30:27,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24959/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24959/checkm_input OceanDNA-b24959/checkm_result
[2023-03-14 12:31:21,317] [INFO] Task succeeded: CheckM
[2023-03-14 12:31:21,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:31:21,326] [INFO] ===== Completeness check finished =====
[2023-03-14 12:31:21,326] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:31:21,326] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24959/markers.fasta)
[2023-03-14 12:31:21,327] [INFO] Task started: Blastn
[2023-03-14 12:31:21,327] [INFO] Running command: blastn -query OceanDNA-b24959/markers.fasta -db /var/lib/cwl/stg276b3fd4-37d2-44d3-b033-c6861ec414ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24959/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:31:23,080] [INFO] Task succeeded: Blastn
[2023-03-14 12:31:23,083] [INFO] Selected 10 target genomes.
[2023-03-14 12:31:23,083] [INFO] Target genome list was writen to OceanDNA-b24959/target_genomes_gtdb.txt
[2023-03-14 12:31:23,120] [INFO] Task started: fastANI
[2023-03-14 12:31:23,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgab2a0a51-3924-4dcc-b53a-13f687cad694/OceanDNA-b24959.fa --refList OceanDNA-b24959/target_genomes_gtdb.txt --output OceanDNA-b24959/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:31:30,644] [INFO] Task succeeded: fastANI
[2023-03-14 12:31:30,651] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:31:30,651] [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_002480495.1	s__Parvibaculum sp002480495	99.977	1163	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	conclusive
GCA_002842875.1	s__Parvibaculum sp002842875	83.9494	760	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	83.7208	846	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_014359855.1	s__Parvibaculum sp014359855	83.6034	512	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694985.1	s__Parvibaculum sp002694985	83.5681	810	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	81.9459	777	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823365.1	s__Parvibaculum sp013823365	81.786	586	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000314675.2	s__Afipia broomeae	76.3135	134	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	97.99	97.77	0.89	0.84	9	-
GCF_014635285.1	s__Stappia taiwanensis	76.2776	134	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003133345.1	s__Pseudolabrys sp003133345	75.9628	92	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	96.45	96.45	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:31:30,652] [INFO] GTDB search result was written to OceanDNA-b24959/result_gtdb.tsv
[2023-03-14 12:31:30,652] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:31:30,655] [INFO] DFAST_QC result json was written to OceanDNA-b24959/dqc_result.json
[2023-03-14 12:31:30,655] [INFO] DFAST_QC completed!
[2023-03-14 12:31:30,655] [INFO] Total running time: 0h1m45s