[2023-03-15 03:14:16,319] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,319] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference
[2023-03-15 03:14:17,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,550] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,550] [INFO] Running command: cat /var/lib/cwl/stg15898379-2078-4620-a693-953a7df33956/OceanDNA-b24705.fa | prodigal -d OceanDNA-b24705/cds.fna -a OceanDNA-b24705/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:37,513] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:37,514] [INFO] Task started: HMMsearch
[2023-03-15 03:14:37,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b24705/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/reference_markers.hmm OceanDNA-b24705/protein.faa > /dev/null
[2023-03-15 03:14:37,808] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:37,809] [INFO] Found 6/6 markers.
[2023-03-15 03:14:37,830] [INFO] Query marker FASTA was written to OceanDNA-b24705/markers.fasta
[2023-03-15 03:14:37,830] [INFO] Task started: Blastn
[2023-03-15 03:14:37,830] [INFO] Running command: blastn -query OceanDNA-b24705/markers.fasta -db /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/reference_markers.fasta -out OceanDNA-b24705/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:38,649] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:38,650] [INFO] Selected 30 target genomes.
[2023-03-15 03:14:38,650] [INFO] Target genome list was writen to OceanDNA-b24705/target_genomes.txt
[2023-03-15 03:14:38,685] [INFO] Task started: fastANI
[2023-03-15 03:14:38,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg15898379-2078-4620-a693-953a7df33956/OceanDNA-b24705.fa --refList OceanDNA-b24705/target_genomes.txt --output OceanDNA-b24705/fastani_result.tsv --threads 1
[2023-03-15 03:15:04,520] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:04,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:15:04,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:15:04,535] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:15:04,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:15:04,535] [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
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.5231	100	1053	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.4437	117	1053	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.4189	118	1053	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4024	108	1053	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.3677	108	1053	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.3526	127	1053	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.2754	72	1053	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.2611	119	1053	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.2348	119	1053	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.1307	118	1053	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	76.1306	75	1053	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.0906	129	1053	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	76.0874	72	1053	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.0565	80	1053	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.0513	126	1053	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.0353	66	1053	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.0228	81	1053	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.0167	93	1053	95	below_threshold
Bradyrhizobium betae	strain=PL7HG1	GCA_008932115.1	244734	244734	type	True	76.0157	77	1053	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	76.0007	90	1053	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.9405	97	1053	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.9287	96	1053	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	75.9275	75	1053	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.9207	115	1053	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.907	62	1053	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.8764	79	1053	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.5674	63	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:15:04,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24705/tc_result.tsv
[2023-03-15 03:15:04,536] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:15:04,536] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:15:04,536] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/checkm_data
[2023-03-15 03:15:04,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:15:04,541] [INFO] Task started: CheckM
[2023-03-15 03:15:04,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24705/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24705/checkm_input OceanDNA-b24705/checkm_result
[2023-03-15 03:15:53,986] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:53,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:53,989] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:53,989] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:53,989] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24705/markers.fasta)
[2023-03-15 03:15:53,989] [INFO] Task started: Blastn
[2023-03-15 03:15:53,989] [INFO] Running command: blastn -query OceanDNA-b24705/markers.fasta -db /var/lib/cwl/stg3f1a3b89-49a4-4b7a-87b7-3e066a823704/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24705/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:55,537] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:55,538] [INFO] Selected 14 target genomes.
[2023-03-15 03:15:55,538] [INFO] Target genome list was writen to OceanDNA-b24705/target_genomes_gtdb.txt
[2023-03-15 03:15:55,583] [INFO] Task started: fastANI
[2023-03-15 03:15:55,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg15898379-2078-4620-a693-953a7df33956/OceanDNA-b24705.fa --refList OceanDNA-b24705/target_genomes_gtdb.txt --output OceanDNA-b24705/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:16:04,506] [INFO] Task succeeded: fastANI
[2023-03-15 03:16:04,514] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:16:04,514] [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_016124645.1	s__UBA2020 sp016124645	79.5049	427	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297545.1	s__UBA2020 sp004297545	78.8829	425	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794125.1	s__UBA2020 sp016794125	78.7336	475	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971405.1	s__PALSA-926 sp018971405	77.7829	175	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__PALSA-926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003524565.1	s__UBA2020 sp003524565	77.511	175	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002334985.1	s__UBA2020 sp002334985	77.2072	223	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micavibrionales;f__UBA2020;g__UBA2020	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827795.1	s__Azospirillum brasilense_E	76.3699	106	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_900230255.1	s__Caenispirillum bisanense	76.2341	138	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	76.0512	120	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	76.0166	93	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	75.8339	83	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	75.7446	60	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	75.0797	57	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:16:04,514] [INFO] GTDB search result was written to OceanDNA-b24705/result_gtdb.tsv
[2023-03-15 03:16:04,515] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:16:04,517] [INFO] DFAST_QC result json was written to OceanDNA-b24705/dqc_result.json
[2023-03-15 03:16:04,517] [INFO] DFAST_QC completed!
[2023-03-15 03:16:04,517] [INFO] Total running time: 0h1m48s