[2023-03-14 14:09:10,705] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:09:10,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:09:10,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference
[2023-03-14 14:09:12,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:09:12,146] [INFO] Task started: Prodigal
[2023-03-14 14:09:12,147] [INFO] Running command: cat /var/lib/cwl/stgbf06f809-239e-4e45-a405-ecb831c6e0cd/OceanDNA-b24902.fa | prodigal -d OceanDNA-b24902/cds.fna -a OceanDNA-b24902/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:09:39,086] [INFO] Task succeeded: Prodigal
[2023-03-14 14:09:39,086] [INFO] Task started: HMMsearch
[2023-03-14 14:09:39,086] [INFO] Running command: hmmsearch --tblout OceanDNA-b24902/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/reference_markers.hmm OceanDNA-b24902/protein.faa > /dev/null
[2023-03-14 14:09:39,281] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:09:39,281] [INFO] Found 6/6 markers.
[2023-03-14 14:09:39,301] [INFO] Query marker FASTA was written to OceanDNA-b24902/markers.fasta
[2023-03-14 14:09:39,302] [INFO] Task started: Blastn
[2023-03-14 14:09:39,302] [INFO] Running command: blastn -query OceanDNA-b24902/markers.fasta -db /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/reference_markers.fasta -out OceanDNA-b24902/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:09:40,138] [INFO] Task succeeded: Blastn
[2023-03-14 14:09:40,139] [INFO] Selected 23 target genomes.
[2023-03-14 14:09:40,139] [INFO] Target genome list was writen to OceanDNA-b24902/target_genomes.txt
[2023-03-14 14:09:40,150] [INFO] Task started: fastANI
[2023-03-14 14:09:40,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf06f809-239e-4e45-a405-ecb831c6e0cd/OceanDNA-b24902.fa --refList OceanDNA-b24902/target_genomes.txt --output OceanDNA-b24902/fastani_result.tsv --threads 1
[2023-03-14 14:10:07,736] [INFO] Task succeeded: fastANI
[2023-03-14 14:10:07,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:10:07,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:10:07,750] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:10:07,750] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:10:07,750] [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	80.8731	635	1012	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	78.5068	456	1012	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	78.3208	401	1012	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	77.0504	254	1012	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.8461	148	1012	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.4724	128	1012	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.4432	144	1012	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.3776	108	1012	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	76.3598	109	1012	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	76.3404	141	1012	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.2549	132	1012	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.2034	129	1012	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	76.0779	139	1012	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	76.0615	136	1012	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	76.0476	151	1012	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.003	111	1012	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	76.0014	115	1012	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	75.9974	117	1012	95	below_threshold
Microvirga antarctica	strain=3D7	GCA_017921815.1	2819233	2819233	type	True	75.8334	92	1012	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	75.6444	71	1012	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	75.6305	88	1012	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	75.6075	65	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:10:07,751] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24902/tc_result.tsv
[2023-03-14 14:10:07,752] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:10:07,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:10:07,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/checkm_data
[2023-03-14 14:10:07,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:10:07,901] [INFO] Task started: CheckM
[2023-03-14 14:10:07,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24902/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24902/checkm_input OceanDNA-b24902/checkm_result
[2023-03-14 14:10:57,077] [INFO] Task succeeded: CheckM
[2023-03-14 14:10:57,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:10:57,080] [INFO] ===== Completeness check finished =====
[2023-03-14 14:10:57,080] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:10:57,080] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24902/markers.fasta)
[2023-03-14 14:10:57,081] [INFO] Task started: Blastn
[2023-03-14 14:10:57,081] [INFO] Running command: blastn -query OceanDNA-b24902/markers.fasta -db /var/lib/cwl/stg0ca4d84a-cc4d-43fb-be15-054cf59cd73b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24902/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:10:58,714] [INFO] Task succeeded: Blastn
[2023-03-14 14:10:58,715] [INFO] Selected 12 target genomes.
[2023-03-14 14:10:58,715] [INFO] Target genome list was writen to OceanDNA-b24902/target_genomes_gtdb.txt
[2023-03-14 14:10:58,766] [INFO] Task started: fastANI
[2023-03-14 14:10:58,766] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf06f809-239e-4e45-a405-ecb831c6e0cd/OceanDNA-b24902.fa --refList OceanDNA-b24902/target_genomes_gtdb.txt --output OceanDNA-b24902/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:11:07,844] [INFO] Task succeeded: fastANI
[2023-03-14 14:11:07,852] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:11:07,852] [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
GCF_000017565.1	s__Parvibaculum lavamentivorans	80.863	636	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	80.5952	587	1012	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	80.4958	635	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002480495.1	s__Parvibaculum sp002480495	80.4575	611	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_014359855.1	s__Parvibaculum sp014359855	80.1605	385	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	80.1349	499	1012	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	80.0439	571	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.99	99.99	0.99	0.99	2	-
GCA_001897755.1	s__Afipia sp001897755	76.5497	119	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900112185.1	s__Bosea sp900112185	76.4764	147	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114915.1	s__Bradyrhizobium guangxiense	76.0615	136	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	75.8175	79	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	75.6908	131	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:11:07,852] [INFO] GTDB search result was written to OceanDNA-b24902/result_gtdb.tsv
[2023-03-14 14:11:07,852] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:11:07,855] [INFO] DFAST_QC result json was written to OceanDNA-b24902/dqc_result.json
[2023-03-14 14:11:07,855] [INFO] DFAST_QC completed!
[2023-03-14 14:11:07,855] [INFO] Total running time: 0h1m57s