[2023-03-18 05:35:37,306] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,308] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference
[2023-03-18 05:35:38,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,965] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,965] [INFO] Running command: cat /var/lib/cwl/stg1d14d813-1d92-4c03-9768-414628c4d531/OceanDNA-b33062.fa | prodigal -d OceanDNA-b33062/cds.fna -a OceanDNA-b33062/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:49,221] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:49,221] [INFO] Task started: HMMsearch
[2023-03-18 05:35:49,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b33062/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/reference_markers.hmm OceanDNA-b33062/protein.faa > /dev/null
[2023-03-18 05:35:49,396] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:49,396] [INFO] Found 6/6 markers.
[2023-03-18 05:35:49,430] [INFO] Query marker FASTA was written to OceanDNA-b33062/markers.fasta
[2023-03-18 05:35:49,431] [INFO] Task started: Blastn
[2023-03-18 05:35:49,431] [INFO] Running command: blastn -query OceanDNA-b33062/markers.fasta -db /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/reference_markers.fasta -out OceanDNA-b33062/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:50,003] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:50,007] [INFO] Selected 30 target genomes.
[2023-03-18 05:35:50,007] [INFO] Target genome list was writen to OceanDNA-b33062/target_genomes.txt
[2023-03-18 05:35:50,025] [INFO] Task started: fastANI
[2023-03-18 05:35:50,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d14d813-1d92-4c03-9768-414628c4d531/OceanDNA-b33062.fa --refList OceanDNA-b33062/target_genomes.txt --output OceanDNA-b33062/fastani_result.tsv --threads 1
[2023-03-18 05:36:11,530] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:11,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:11,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:11,537] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:11,537] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:11,537] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9432	65	472	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.8317	81	472	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.6771	58	472	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.4496	52	472	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.4215	64	472	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.3222	50	472	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.1802	75	472	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.1564	74	472	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:11,539] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33062/tc_result.tsv
[2023-03-18 05:36:11,541] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:11,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:11,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/checkm_data
[2023-03-18 05:36:11,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:11,550] [INFO] Task started: CheckM
[2023-03-18 05:36:11,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33062/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33062/checkm_input OceanDNA-b33062/checkm_result
[2023-03-18 05:36:41,479] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:41,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:41,573] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:41,573] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:41,573] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33062/markers.fasta)
[2023-03-18 05:36:41,574] [INFO] Task started: Blastn
[2023-03-18 05:36:41,574] [INFO] Running command: blastn -query OceanDNA-b33062/markers.fasta -db /var/lib/cwl/stg4f2a9bb6-9074-4c0f-a0af-8067d80a4a39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33062/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:42,451] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:42,452] [INFO] Selected 24 target genomes.
[2023-03-18 05:36:42,453] [INFO] Target genome list was writen to OceanDNA-b33062/target_genomes_gtdb.txt
[2023-03-18 05:36:42,535] [INFO] Task started: fastANI
[2023-03-18 05:36:42,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d14d813-1d92-4c03-9768-414628c4d531/OceanDNA-b33062.fa --refList OceanDNA-b33062/target_genomes_gtdb.txt --output OceanDNA-b33062/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:59,633] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:59,639] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:36:59,640] [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_002937525.1	s__MarineAlpha4-Bin1 sp002937525	97.2674	298	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__MarineAlpha4-Bin1	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_012103325.1	s__GCA-2717185 sp012103325	76.8986	153	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660965.1	s__JABJJH01 sp018660965	76.2961	71	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__JABJJH01	95.0	98.84	98.67	0.82	0.82	3	-
GCA_000518365.1	s__URHD0088 sp000518365	76.1198	73	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015222795.1	s__JADFVY01 sp015222795	76.1148	52	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__JADFVY01;g__JADFVY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	75.8317	81	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_008012315.1	s__SSEL01 sp008012315	75.8179	53	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SSEL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124535.1	s__RI-112 sp016124535	75.6662	50	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__RI-112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.3211	55	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	75.1909	64	472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:59,641] [INFO] GTDB search result was written to OceanDNA-b33062/result_gtdb.tsv
[2023-03-18 05:36:59,641] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:59,643] [INFO] DFAST_QC result json was written to OceanDNA-b33062/dqc_result.json
[2023-03-18 05:36:59,643] [INFO] DFAST_QC completed!
[2023-03-18 05:36:59,643] [INFO] Total running time: 0h1m22s