[2023-03-16 04:54:07,036] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference
[2023-03-16 04:54:08,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,353] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,353] [INFO] Running command: cat /var/lib/cwl/stg2be152af-4680-4c3a-bd87-c59e5be9aef1/OceanDNA-b24595.fa | prodigal -d OceanDNA-b24595/cds.fna -a OceanDNA-b24595/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:32,566] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:32,566] [INFO] Task started: HMMsearch
[2023-03-16 04:54:32,566] [INFO] Running command: hmmsearch --tblout OceanDNA-b24595/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/reference_markers.hmm OceanDNA-b24595/protein.faa > /dev/null
[2023-03-16 04:54:32,848] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:32,849] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2be152af-4680-4c3a-bd87-c59e5be9aef1/OceanDNA-b24595.fa]
[2023-03-16 04:54:32,879] [INFO] Query marker FASTA was written to OceanDNA-b24595/markers.fasta
[2023-03-16 04:54:32,879] [INFO] Task started: Blastn
[2023-03-16 04:54:32,879] [INFO] Running command: blastn -query OceanDNA-b24595/markers.fasta -db /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/reference_markers.fasta -out OceanDNA-b24595/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:33,824] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:33,825] [INFO] Selected 21 target genomes.
[2023-03-16 04:54:33,825] [INFO] Target genome list was writen to OceanDNA-b24595/target_genomes.txt
[2023-03-16 04:54:33,840] [INFO] Task started: fastANI
[2023-03-16 04:54:33,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be152af-4680-4c3a-bd87-c59e5be9aef1/OceanDNA-b24595.fa --refList OceanDNA-b24595/target_genomes.txt --output OceanDNA-b24595/fastani_result.tsv --threads 1
[2023-03-16 04:54:56,441] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:56,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:56,442] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:56,454] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:56,454] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:56,454] [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
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	78.4872	650	1400	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	78.4821	652	1400	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	78.187	465	1400	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.212	497	1400	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	77.1737	328	1400	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.9335	381	1400	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.8079	444	1400	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.7647	442	1400	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.7585	486	1400	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	76.7226	421	1400	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.6999	394	1400	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	76.6828	390	1400	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6589	234	1400	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.5358	447	1400	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.5344	438	1400	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.459	340	1400	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3467	453	1400	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2808	289	1400	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.1619	320	1400	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.0168	308	1400	95	below_threshold
Camelimonas lactis	strain=DSM 22958	GCA_004342915.1	659006	659006	type	True	75.8044	199	1400	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:56,455] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24595/tc_result.tsv
[2023-03-16 04:54:56,455] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:56,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:56,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/checkm_data
[2023-03-16 04:54:56,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:56,531] [INFO] Task started: CheckM
[2023-03-16 04:54:56,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24595/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24595/checkm_input OceanDNA-b24595/checkm_result
[2023-03-16 04:55:53,268] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:53,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:53,272] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:53,272] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:53,272] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24595/markers.fasta)
[2023-03-16 04:55:53,273] [INFO] Task started: Blastn
[2023-03-16 04:55:53,273] [INFO] Running command: blastn -query OceanDNA-b24595/markers.fasta -db /var/lib/cwl/stgc259329a-deac-4173-bd01-ff6cf145dff1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24595/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:55,010] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:55,011] [INFO] Selected 20 target genomes.
[2023-03-16 04:55:55,011] [INFO] Target genome list was writen to OceanDNA-b24595/target_genomes_gtdb.txt
[2023-03-16 04:55:55,039] [INFO] Task started: fastANI
[2023-03-16 04:55:55,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be152af-4680-4c3a-bd87-c59e5be9aef1/OceanDNA-b24595.fa --refList OceanDNA-b24595/target_genomes_gtdb.txt --output OceanDNA-b24595/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:56:14,673] [INFO] Task succeeded: fastANI
[2023-03-16 04:56:14,685] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:56:14,685] [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_014324045.1	s__JACOMY01 sp014324045	79.3325	325	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__JACOMY01;g__JACOMY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	78.4769	654	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_006969625.1	s__Algihabitans sp006969625	78.2419	486	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	78.1734	466	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	77.6232	400	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	77.1832	325	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.1495	509	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.9036	388	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876155.1	s__Azospirillum rugosum	76.8462	436	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989665.1	s__Azospirillum doebereinerae	76.717	422	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	76.7003	455	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365405.1	s__Azospirillum brasilense_D	76.6394	411	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.5281	526	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.3779	248	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.3129	350	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241695.1	s__Hansschlegelia sp003241695	76.069	245	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425365.1	s__Roseococcus flocculans	75.9484	314	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342915.1	s__Camelimonas lactis	75.845	197	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Camelimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016106005.1	s__Roseomonas_B sp016106005	75.8141	278	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	75.7645	196	1400	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:56:14,685] [INFO] GTDB search result was written to OceanDNA-b24595/result_gtdb.tsv
[2023-03-16 04:56:14,685] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:56:14,687] [INFO] DFAST_QC result json was written to OceanDNA-b24595/dqc_result.json
[2023-03-16 04:56:14,688] [INFO] DFAST_QC completed!
[2023-03-16 04:56:14,688] [INFO] Total running time: 0h2m8s