[2023-03-19 04:43:18,675] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference
[2023-03-19 04:43:19,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,797] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,797] [INFO] Running command: cat /var/lib/cwl/stgc1c66a9f-b01d-4c41-8051-c20b02443aac/OceanDNA-b10443.fa | prodigal -d OceanDNA-b10443/cds.fna -a OceanDNA-b10443/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:29,439] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:29,440] [INFO] Task started: HMMsearch
[2023-03-19 04:43:29,440] [INFO] Running command: hmmsearch --tblout OceanDNA-b10443/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/reference_markers.hmm OceanDNA-b10443/protein.faa > /dev/null
[2023-03-19 04:43:29,617] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:29,618] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc1c66a9f-b01d-4c41-8051-c20b02443aac/OceanDNA-b10443.fa]
[2023-03-19 04:43:29,631] [INFO] Query marker FASTA was written to OceanDNA-b10443/markers.fasta
[2023-03-19 04:43:29,631] [INFO] Task started: Blastn
[2023-03-19 04:43:29,631] [INFO] Running command: blastn -query OceanDNA-b10443/markers.fasta -db /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/reference_markers.fasta -out OceanDNA-b10443/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:30,202] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:30,202] [INFO] Selected 13 target genomes.
[2023-03-19 04:43:30,203] [INFO] Target genome list was writen to OceanDNA-b10443/target_genomes.txt
[2023-03-19 04:43:30,238] [INFO] Task started: fastANI
[2023-03-19 04:43:30,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c66a9f-b01d-4c41-8051-c20b02443aac/OceanDNA-b10443.fa --refList OceanDNA-b10443/target_genomes.txt --output OceanDNA-b10443/fastani_result.tsv --threads 1
[2023-03-19 04:43:37,909] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:37,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:37,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:37,919] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 04:43:37,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 04:43:37,919] [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
Tenacibaculum discolor	strain=DSM 18842	GCA_003664185.1	361581	361581	type	True	98.2246	482	508	95	conclusive
Tenacibaculum singaporense	strain=DSM 106434	GCA_003867015.1	2358479	2358479	type	True	89.9615	463	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_003867075.1	104268	104268	type	True	89.0756	442	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_900129475.1	104268	104268	type	True	89.0606	445	508	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	88.9662	439	508	95	below_threshold
Tenacibaculum gallaicum	strain=DSM 18841	GCA_003387615.1	561505	561505	type	True	88.9529	453	508	95	below_threshold
Tenacibaculum lutimaris	strain=DSM 16505	GCA_003610735.1	285258	285258	type	True	88.0655	418	508	95	below_threshold
Tenacibaculum caenipelagi	strain=CECT 8283	GCA_004363005.1	1325435	1325435	type	True	84.2534	422	508	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	79.3595	307	508	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	78.193	222	508	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.8309	232	508	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.4025	174	508	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.3004	166	508	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:37,919] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10443/tc_result.tsv
[2023-03-19 04:43:37,919] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:37,919] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:37,919] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/checkm_data
[2023-03-19 04:43:37,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:38,008] [INFO] Task started: CheckM
[2023-03-19 04:43:38,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10443/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10443/checkm_input OceanDNA-b10443/checkm_result
[2023-03-19 04:44:06,537] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:06,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:06,540] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:06,540] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:06,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10443/markers.fasta)
[2023-03-19 04:44:06,541] [INFO] Task started: Blastn
[2023-03-19 04:44:06,541] [INFO] Running command: blastn -query OceanDNA-b10443/markers.fasta -db /var/lib/cwl/stg62bd2bb7-81e4-4bcb-9ad1-7ad9506752ad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10443/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:07,388] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:07,389] [INFO] Selected 6 target genomes.
[2023-03-19 04:44:07,389] [INFO] Target genome list was writen to OceanDNA-b10443/target_genomes_gtdb.txt
[2023-03-19 04:44:07,420] [INFO] Task started: fastANI
[2023-03-19 04:44:07,420] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1c66a9f-b01d-4c41-8051-c20b02443aac/OceanDNA-b10443.fa --refList OceanDNA-b10443/target_genomes_gtdb.txt --output OceanDNA-b10443/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:11,202] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:11,206] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:44:11,206] [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_003664185.1	s__Tenacibaculum discolor	98.2246	482	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.93	97.89	0.89	0.88	3	conclusive
GCF_003867015.1	s__Tenacibaculum singaporense	89.9332	464	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	96.88	96.88	0.91	0.91	2	-
GCF_003867075.1	s__Tenacibaculum mesophilum	89.0756	442	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	99.18	98.30	0.96	0.93	5	-
GCF_003387615.1	s__Tenacibaculum gallaicum	88.9529	453	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610735.1	s__Tenacibaculum lutimaris	88.0655	418	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	97.15	97.15	0.89	0.89	2	-
GCF_004363005.1	s__Tenacibaculum caenipelagi	84.2534	422	508	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:11,207] [INFO] GTDB search result was written to OceanDNA-b10443/result_gtdb.tsv
[2023-03-19 04:44:11,207] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:11,208] [INFO] DFAST_QC result json was written to OceanDNA-b10443/dqc_result.json
[2023-03-19 04:44:11,208] [INFO] DFAST_QC completed!
[2023-03-19 04:44:11,208] [INFO] Total running time: 0h0m53s