[2023-03-15 14:37:49,313] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:49,313] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:49,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference
[2023-03-15 14:37:50,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:50,420] [INFO] Task started: Prodigal
[2023-03-15 14:37:50,420] [INFO] Running command: cat /var/lib/cwl/stg9f89c91e-0ca4-423b-811a-fa75891a341d/OceanDNA-b26421.fa | prodigal -d OceanDNA-b26421/cds.fna -a OceanDNA-b26421/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:04,032] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:04,032] [INFO] Task started: HMMsearch
[2023-03-15 14:38:04,032] [INFO] Running command: hmmsearch --tblout OceanDNA-b26421/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/reference_markers.hmm OceanDNA-b26421/protein.faa > /dev/null
[2023-03-15 14:38:04,217] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:04,218] [INFO] Found 6/6 markers.
[2023-03-15 14:38:04,233] [INFO] Query marker FASTA was written to OceanDNA-b26421/markers.fasta
[2023-03-15 14:38:04,234] [INFO] Task started: Blastn
[2023-03-15 14:38:04,234] [INFO] Running command: blastn -query OceanDNA-b26421/markers.fasta -db /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/reference_markers.fasta -out OceanDNA-b26421/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:04,940] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:04,940] [INFO] Selected 32 target genomes.
[2023-03-15 14:38:04,941] [INFO] Target genome list was writen to OceanDNA-b26421/target_genomes.txt
[2023-03-15 14:38:04,960] [INFO] Task started: fastANI
[2023-03-15 14:38:04,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f89c91e-0ca4-423b-811a-fa75891a341d/OceanDNA-b26421.fa --refList OceanDNA-b26421/target_genomes.txt --output OceanDNA-b26421/fastani_result.tsv --threads 1
[2023-03-15 14:38:30,463] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:30,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:38:30,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:30,475] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:30,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:38:30,475] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1939	69	701	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.1691	66	701	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.1256	77	701	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.8942	86	701	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.8387	66	701	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.7952	57	701	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.7286	54	701	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.7242	66	701	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.7186	69	701	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	75.5547	54	701	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.5103	58	701	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.343	73	701	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	75.3105	53	701	95	below_threshold
Niveispirillum cyanobacteriorum	strain=TH16	GCA_002868735.1	1612173	1612173	type	True	75.2983	54	701	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.2868	71	701	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.1895	60	701	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.08	65	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:30,475] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26421/tc_result.tsv
[2023-03-15 14:38:30,476] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:30,476] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:30,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/checkm_data
[2023-03-15 14:38:30,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:30,717] [INFO] Task started: CheckM
[2023-03-15 14:38:30,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26421/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26421/checkm_input OceanDNA-b26421/checkm_result
[2023-03-15 14:39:08,627] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:08,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:08,634] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:08,635] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:08,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26421/markers.fasta)
[2023-03-15 14:39:08,636] [INFO] Task started: Blastn
[2023-03-15 14:39:08,636] [INFO] Running command: blastn -query OceanDNA-b26421/markers.fasta -db /var/lib/cwl/stg3f4825ec-39d3-48ce-bcbe-9ec24a3074e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26421/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:10,024] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:10,025] [INFO] Selected 14 target genomes.
[2023-03-15 14:39:10,025] [INFO] Target genome list was writen to OceanDNA-b26421/target_genomes_gtdb.txt
[2023-03-15 14:39:10,039] [INFO] Task started: fastANI
[2023-03-15 14:39:10,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f89c91e-0ca4-423b-811a-fa75891a341d/OceanDNA-b26421.fa --refList OceanDNA-b26421/target_genomes_gtdb.txt --output OceanDNA-b26421/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:17,709] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:17,714] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:17,714] [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_004213025.1	s__UBA8309 sp004213025	98.8962	295	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009920665.1	s__UBA8309 sp009920665	85.8688	550	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	85.1063	543	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011522725.1	s__UBA8309 sp001627655	80.0956	386	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.91	98.58	0.92	0.89	8	-
GCA_002457745.1	s__UBA8309 sp002457745	79.9755	298	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	78.191	178	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_016780765.1	s__UBA8309 sp016780765	78.0814	236	701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:17,715] [INFO] GTDB search result was written to OceanDNA-b26421/result_gtdb.tsv
[2023-03-15 14:39:17,716] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:17,717] [INFO] DFAST_QC result json was written to OceanDNA-b26421/dqc_result.json
[2023-03-15 14:39:17,717] [INFO] DFAST_QC completed!
[2023-03-15 14:39:17,718] [INFO] Total running time: 0h1m28s