[2023-03-17 06:30:49,086] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,086] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,292] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg9408e16c-8846-47a8-9d87-589dccb0849d/OceanDNA-b26774.fa | prodigal -d OceanDNA-b26774/cds.fna -a OceanDNA-b26774/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:02,844] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:02,844] [INFO] Task started: HMMsearch
[2023-03-17 06:31:02,844] [INFO] Running command: hmmsearch --tblout OceanDNA-b26774/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/reference_markers.hmm OceanDNA-b26774/protein.faa > /dev/null
[2023-03-17 06:31:03,029] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:03,030] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9408e16c-8846-47a8-9d87-589dccb0849d/OceanDNA-b26774.fa]
[2023-03-17 06:31:03,050] [INFO] Query marker FASTA was written to OceanDNA-b26774/markers.fasta
[2023-03-17 06:31:03,050] [INFO] Task started: Blastn
[2023-03-17 06:31:03,050] [INFO] Running command: blastn -query OceanDNA-b26774/markers.fasta -db /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/reference_markers.fasta -out OceanDNA-b26774/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:03,747] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:03,748] [INFO] Selected 34 target genomes.
[2023-03-17 06:31:03,748] [INFO] Target genome list was writen to OceanDNA-b26774/target_genomes.txt
[2023-03-17 06:31:03,765] [INFO] Task started: fastANI
[2023-03-17 06:31:03,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg9408e16c-8846-47a8-9d87-589dccb0849d/OceanDNA-b26774.fa --refList OceanDNA-b26774/target_genomes.txt --output OceanDNA-b26774/fastani_result.tsv --threads 1
[2023-03-17 06:31:34,826] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:34,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:34,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:34,844] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:34,844] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:34,844] [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
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.8611	126	672	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	76.8242	128	672	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.5799	191	672	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	76.5756	134	672	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	76.5493	116	672	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	76.4203	150	672	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.3927	150	672	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	76.3598	115	672	95	below_threshold
Chelativorans xinjiangense	strain=lm93	GCA_009812055.1	2681485	2681485	type	True	76.3317	146	672	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	76.2777	120	672	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.2322	87	672	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	76.2073	113	672	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	76.0429	120	672	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.9893	157	672	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	75.9851	103	672	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.9719	123	672	95	below_threshold
Pararhizobium mangrovi	strain=BGMRC 6574	GCA_006516965.1	2590452	2590452	type	True	75.9691	119	672	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	75.9389	158	672	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	75.8926	106	672	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	75.8608	165	672	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.8086	156	672	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	75.7963	157	672	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	75.756	170	672	95	below_threshold
Methylobacterium frigidaeris	strain=IER25-16	GCA_002759055.1	2038277	2038277	type	True	75.7426	104	672	95	below_threshold
Methylobacterium brachiatum	strain=B0021	GCA_020523825.1	269660	269660	type	True	75.7416	126	672	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	75.7359	160	672	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.7223	181	672	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	75.7192	150	672	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	75.7132	163	672	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.7119	120	672	95	below_threshold
Methylobacterium variabile	strain=DSM 16961	GCA_001043975.1	298794	298794	type	True	75.6662	155	672	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.51	153	672	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.5052	126	672	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.4463	129	672	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:34,844] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26774/tc_result.tsv
[2023-03-17 06:31:34,844] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:34,844] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:34,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/checkm_data
[2023-03-17 06:31:34,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:34,849] [INFO] Task started: CheckM
[2023-03-17 06:31:34,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26774/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26774/checkm_input OceanDNA-b26774/checkm_result
[2023-03-17 06:32:09,027] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:09,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:09,030] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:09,030] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:09,030] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26774/markers.fasta)
[2023-03-17 06:32:09,030] [INFO] Task started: Blastn
[2023-03-17 06:32:09,030] [INFO] Running command: blastn -query OceanDNA-b26774/markers.fasta -db /var/lib/cwl/stgdf5582ea-0e5c-43ae-8adc-bee5dccc8ec9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26774/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:10,211] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:10,212] [INFO] Selected 34 target genomes.
[2023-03-17 06:32:10,212] [INFO] Target genome list was writen to OceanDNA-b26774/target_genomes_gtdb.txt
[2023-03-17 06:32:10,612] [INFO] Task started: fastANI
[2023-03-17 06:32:10,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg9408e16c-8846-47a8-9d87-589dccb0849d/OceanDNA-b26774.fa --refList OceanDNA-b26774/target_genomes_gtdb.txt --output OceanDNA-b26774/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:40,375] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:40,393] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:40,393] [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_003577315.1	s__Aquamicrobium_A sp003577315	76.9449	194	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	76.8059	129	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	76.582	129	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_003863365.1	s__Mesorhizobium tamadayense	76.5468	116	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952525.1	s__Mesorhizobium sp002294945	76.5105	109	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.39	99.02	0.88	0.85	8	-
GCF_003952385.1	s__Mesorhizobium sp003952385	76.4784	129	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_003952505.1	s__Mesorhizobium sp003952505	76.4689	115	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_017815135.1	s__Jiella sp017815135	76.4382	107	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	76.4337	149	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_003258835.1	s__Rhodobium orientis	76.2905	141	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_014843825.1	s__Mesorhizobium silamurunense	76.2778	120	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.52	99.52	0.90	0.90	2	-
GCF_001463705.1	s__Aureimonas sp001463705	76.2422	135	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	76.2385	120	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	76.2194	144	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711085.1	s__JADJTR01 sp016711085	76.1824	97	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__JADJTR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	76.1495	92	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	76.1244	125	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	76.1174	115	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	76.1062	147	672	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_002295115.1	s__Mesorhizobium sp002295115	75.9796	122	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.79	96.42	0.94	0.85	9	-
GCF_001305515.1	s__Prosthecomicrobium_A hirschii	75.9736	164	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	97.89	97.89	0.95	0.95	2	-
GCF_006516965.1	s__Pararhizobium_B mangrovi	75.9691	119	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	75.936	158	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702305.1	s__GCF-000702305 sp000702305	75.879	153	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__GCF-000702305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	75.8597	115	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	75.8038	158	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003096615.1	s__Methylobacterium organophilum	75.7868	156	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.99	98.85	0.91	0.88	18	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.7549	121	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574465.1	s__Methylobacterium crusticola	75.7502	171	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	75.747	182	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_002759055.1	s__Methylobacterium frigidaeris	75.7431	104	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	75.6908	153	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
GCF_900103195.1	s__Methylobacterium sp900103195	75.5844	127	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	96.81	96.81	0.87	0.87	2	-
GCF_001455965.1	s__Methylobacterium sp001455965	75.2671	105	672	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:40,394] [INFO] GTDB search result was written to OceanDNA-b26774/result_gtdb.tsv
[2023-03-17 06:32:40,394] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:40,397] [INFO] DFAST_QC result json was written to OceanDNA-b26774/dqc_result.json
[2023-03-17 06:32:40,397] [INFO] DFAST_QC completed!
[2023-03-17 06:32:40,397] [INFO] Total running time: 0h1m51s