[2023-03-17 10:08:39,122] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,123] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference
[2023-03-17 10:08:40,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,238] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,238] [INFO] Running command: cat /var/lib/cwl/stg711f158d-6948-43a6-91f2-4e9eeb1e9ca7/OceanDNA-b33033.fa | prodigal -d OceanDNA-b33033/cds.fna -a OceanDNA-b33033/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:09:03,954] [INFO] Task succeeded: Prodigal
[2023-03-17 10:09:03,954] [INFO] Task started: HMMsearch
[2023-03-17 10:09:03,954] [INFO] Running command: hmmsearch --tblout OceanDNA-b33033/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/reference_markers.hmm OceanDNA-b33033/protein.faa > /dev/null
[2023-03-17 10:09:04,167] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:09:04,167] [INFO] Found 6/6 markers.
[2023-03-17 10:09:04,190] [INFO] Query marker FASTA was written to OceanDNA-b33033/markers.fasta
[2023-03-17 10:09:04,191] [INFO] Task started: Blastn
[2023-03-17 10:09:04,191] [INFO] Running command: blastn -query OceanDNA-b33033/markers.fasta -db /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/reference_markers.fasta -out OceanDNA-b33033/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:04,853] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:04,854] [INFO] Selected 29 target genomes.
[2023-03-17 10:09:04,854] [INFO] Target genome list was writen to OceanDNA-b33033/target_genomes.txt
[2023-03-17 10:09:04,969] [INFO] Task started: fastANI
[2023-03-17 10:09:04,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg711f158d-6948-43a6-91f2-4e9eeb1e9ca7/OceanDNA-b33033.fa --refList OceanDNA-b33033/target_genomes.txt --output OceanDNA-b33033/fastani_result.tsv --threads 1
[2023-03-17 10:09:24,812] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:24,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:09:24,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:09:24,818] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:09:24,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:09:24,818] [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
Pacificispira spongiicola	strain=KN72	GCA_012926505.1	2729598	2729598	type	True	77.2912	327	1258	95	below_threshold
Hwanghaeella grinnelliae	strain=Gri0909	GCA_004005845.1	2500179	2500179	type	True	76.2684	103	1258	95	below_threshold
Aestuariispira insulae	strain=CECT 8488	GCA_003385955.1	1461337	1461337	type	True	75.9777	99	1258	95	below_threshold
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	75.8295	78	1258	95	below_threshold
Marivibrio halodurans	strain=CGMCC 1.15697	GCA_017963645.1	2039722	2039722	type	True	75.7946	110	1258	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.5547	65	1258	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	75.3147	50	1258	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.2577	62	1258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:09:24,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33033/tc_result.tsv
[2023-03-17 10:09:24,818] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:09:24,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:09:24,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/checkm_data
[2023-03-17 10:09:24,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:09:24,827] [INFO] Task started: CheckM
[2023-03-17 10:09:24,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33033/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33033/checkm_input OceanDNA-b33033/checkm_result
[2023-03-17 10:10:24,262] [INFO] Task succeeded: CheckM
[2023-03-17 10:10:24,262] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:10:24,300] [INFO] ===== Completeness check finished =====
[2023-03-17 10:10:24,300] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:10:24,300] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33033/markers.fasta)
[2023-03-17 10:10:24,301] [INFO] Task started: Blastn
[2023-03-17 10:10:24,301] [INFO] Running command: blastn -query OceanDNA-b33033/markers.fasta -db /var/lib/cwl/stg8712129e-9baa-4236-9b04-b2dcc83033d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33033/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:10:25,454] [INFO] Task succeeded: Blastn
[2023-03-17 10:10:25,455] [INFO] Selected 11 target genomes.
[2023-03-17 10:10:25,455] [INFO] Target genome list was writen to OceanDNA-b33033/target_genomes_gtdb.txt
[2023-03-17 10:10:25,467] [INFO] Task started: fastANI
[2023-03-17 10:10:25,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg711f158d-6948-43a6-91f2-4e9eeb1e9ca7/OceanDNA-b33033.fa --refList OceanDNA-b33033/target_genomes_gtdb.txt --output OceanDNA-b33033/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:10:35,049] [INFO] Task succeeded: fastANI
[2023-03-17 10:10:35,054] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:10:35,054] [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_002709955.1	s__GCA-2696645 sp002709955	99.9652	1247	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.86	99.71	0.96	0.91	10	conclusive
GCA_002696645.1	s__GCA-2696645 sp002696645	90.7946	1079	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	99.85	99.85	0.96	0.96	2	-
GCA_017792345.1	s__GCA-2696645 sp017792345	77.3036	387	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	95.39	95.37	0.96	0.95	3	-
GCA_012926505.1	s__GCA-2696645 sp012926505	77.2997	326	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__GCA-2696645	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005845.1	s__Hwanghaeella grinnelliae	76.2185	106	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__Hwanghaeella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006844765.1	s__SPJV01 sp006844765	76.1742	86	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2696645;g__SPJV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:10:35,054] [INFO] GTDB search result was written to OceanDNA-b33033/result_gtdb.tsv
[2023-03-17 10:10:35,054] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:10:35,055] [INFO] DFAST_QC result json was written to OceanDNA-b33033/dqc_result.json
[2023-03-17 10:10:35,055] [INFO] DFAST_QC completed!
[2023-03-17 10:10:35,055] [INFO] Total running time: 0h1m56s