[2023-03-19 02:40:15,863] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,864] [INFO] DQC Reference Directory: /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference
[2023-03-19 02:40:17,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,563] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,563] [INFO] Running command: cat /var/lib/cwl/stga4b55fbf-0331-476f-9943-4b0452b117f0/OceanDNA-b26737.fa | prodigal -d OceanDNA-b26737/cds.fna -a OceanDNA-b26737/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:43,488] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:43,488] [INFO] Task started: HMMsearch
[2023-03-19 02:40:43,488] [INFO] Running command: hmmsearch --tblout OceanDNA-b26737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/reference_markers.hmm OceanDNA-b26737/protein.faa > /dev/null
[2023-03-19 02:40:43,710] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:43,711] [INFO] Found 6/6 markers.
[2023-03-19 02:40:43,742] [INFO] Query marker FASTA was written to OceanDNA-b26737/markers.fasta
[2023-03-19 02:40:43,743] [INFO] Task started: Blastn
[2023-03-19 02:40:43,743] [INFO] Running command: blastn -query OceanDNA-b26737/markers.fasta -db /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/reference_markers.fasta -out OceanDNA-b26737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:44,461] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:44,464] [INFO] Selected 34 target genomes.
[2023-03-19 02:40:44,465] [INFO] Target genome list was writen to OceanDNA-b26737/target_genomes.txt
[2023-03-19 02:40:44,486] [INFO] Task started: fastANI
[2023-03-19 02:40:44,486] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b55fbf-0331-476f-9943-4b0452b117f0/OceanDNA-b26737.fa --refList OceanDNA-b26737/target_genomes.txt --output OceanDNA-b26737/fastani_result.tsv --threads 1
[2023-03-19 02:41:08,808] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:08,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:41:08,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:41:08,826] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:41:08,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:41:08,827] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.2143	91	1354	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	76.1023	79	1354	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.9885	77	1354	95	below_threshold
Phyllobacterium zundukense	strain=Tri-48; RCAM 03910	GCA_002764115.1	1867719	1867719	type	True	75.9221	67	1354	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.9013	59	1354	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	75.8116	71	1354	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	75.7998	71	1354	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	75.7955	61	1354	95	below_threshold
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	75.7812	72	1354	95	below_threshold
Phyllobacterium sophorae	strain=CCBAU 03422	GCA_003010965.1	1520277	1520277	type	True	75.7623	51	1354	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	75.757	66	1354	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	75.721	53	1354	95	below_threshold
Phyllobacterium pellucidum	strain=BT25	GCA_013327855.1	2740464	2740464	type	True	75.7159	74	1354	95	below_threshold
Brucella ovis	strain=ATCC 25840	GCA_000016845.1	236	236	type	True	75.6845	72	1354	95	below_threshold
Phyllobacterium phragmitis	strain=1N-3	GCA_002980495.1	2670329	2670329	type	True	75.6819	89	1354	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	75.6683	95	1354	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	75.639	92	1354	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	75.639	92	1354	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	75.6126	97	1354	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	75.5713	66	1354	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	75.5694	55	1354	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	75.5496	56	1354	95	below_threshold
Breoghania corrubedonensis	strain=DSM 23382	GCA_003053845.1	665038	665038	type	True	75.5489	70	1354	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	75.5431	56	1354	95	below_threshold
Roseibium hamelinense	strain=ATCC BAA-252	GCA_007830545.1	150831	150831	type	True	75.5141	55	1354	95	below_threshold
Roseibium hamelinense	strain=NBRC 16783	GCA_009711505.1	150831	150831	type	True	75.475	57	1354	95	below_threshold
Roseibium polysiphoniae	strain=KACC 19711	GCA_014842925.1	2571221	2571221	type	True	75.4696	56	1354	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	75.2209	69	1354	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:41:08,829] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26737/tc_result.tsv
[2023-03-19 02:41:08,831] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:41:08,832] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:41:08,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/checkm_data
[2023-03-19 02:41:08,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:41:08,934] [INFO] Task started: CheckM
[2023-03-19 02:41:08,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26737/checkm_input OceanDNA-b26737/checkm_result
[2023-03-19 02:42:13,673] [INFO] Task succeeded: CheckM
[2023-03-19 02:42:13,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:42:13,940] [INFO] ===== Completeness check finished =====
[2023-03-19 02:42:13,940] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:42:13,940] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26737/markers.fasta)
[2023-03-19 02:42:13,941] [INFO] Task started: Blastn
[2023-03-19 02:42:13,941] [INFO] Running command: blastn -query OceanDNA-b26737/markers.fasta -db /var/lib/cwl/stg177c671a-239d-41b2-b013-79b14045543b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:42:15,311] [INFO] Task succeeded: Blastn
[2023-03-19 02:42:15,362] [INFO] Selected 29 target genomes.
[2023-03-19 02:42:15,362] [INFO] Target genome list was writen to OceanDNA-b26737/target_genomes_gtdb.txt
[2023-03-19 02:42:15,392] [INFO] Task started: fastANI
[2023-03-19 02:42:15,392] [INFO] Running command: fastANI --query /var/lib/cwl/stga4b55fbf-0331-476f-9943-4b0452b117f0/OceanDNA-b26737.fa --refList OceanDNA-b26737/target_genomes_gtdb.txt --output OceanDNA-b26737/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:42:38,862] [INFO] Task succeeded: fastANI
[2023-03-19 02:42:38,875] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:42:38,875] [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_016865015.1	s__GCA-2746425 sp016865015	78.8113	496	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__GCA-2746425;g__GCA-2746425	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746425.1	s__GCA-2746425 sp002746425	76.6785	148	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__GCA-2746425;g__GCA-2746425	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	76.1709	70	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCA_903930675.1	s__CAIYZJ01 sp903930675	76.1688	51	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	97.85	97.85	0.78	0.78	2	-
GCF_006440775.1	s__Mesorhizobium sp006440775	76.0847	75	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.82	97.16	0.94	0.92	4	-
GCF_003550135.1	s__Ochrobactrum_B haematophila_B	76.0712	94	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	75.9272	92	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427385.1	s__Mesorhizobium sp001427385	75.9231	58	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519305.1	s__Mesorhizobium ciceri_B	75.9164	76	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001558695.1	s__Paramesorhizobium deserti	75.9052	79	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008107755.1	s__Roseibium sp008107755	75.8468	80	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196455.1	s__Kaistia hirudinis	75.8433	65	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_000429865.1	s__Cucumibacter marinus	75.8132	60	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Cucumibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107695.1	s__Roseibium sp008107695	75.7913	73	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	75.7711	70	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006376685.1	s__Ochrobactrum_B teleogrylli	75.7623	61	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.13	98.09	0.91	0.90	5	-
GCF_003996995.1	s__Mesorhizobium sp003996995	75.7484	79	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.83	97.35	0.87	0.74	32	-
GCF_003601975.1	s__Mesorhizobium waimense	75.6025	98	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103035.1	s__Ochrobactrum oryzae	75.595	68	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.03	98.38	0.88	0.83	3	-
GCA_017307955.1	s__Kaistia sp017307955	75.5807	76	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	75.5496	56	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053845.1	s__Breoghania corrubedonensis	75.5489	70	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716745.1	s__GCA-013693735 sp016716745	75.5241	55	1354	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:42:38,875] [INFO] GTDB search result was written to OceanDNA-b26737/result_gtdb.tsv
[2023-03-19 02:42:38,875] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:42:38,878] [INFO] DFAST_QC result json was written to OceanDNA-b26737/dqc_result.json
[2023-03-19 02:42:38,878] [INFO] DFAST_QC completed!
[2023-03-19 02:42:38,878] [INFO] Total running time: 0h2m23s