[2023-03-19 00:33:19,086] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,087] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,087] [INFO] DQC Reference Directory: /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference
[2023-03-19 00:33:20,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,307] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,307] [INFO] Running command: cat /var/lib/cwl/stg98dc31d9-b10c-457c-bbbb-62696a4f8bb9/OceanDNA-b23275.fa | prodigal -d OceanDNA-b23275/cds.fna -a OceanDNA-b23275/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:47,743] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:47,743] [INFO] Task started: HMMsearch
[2023-03-19 00:33:47,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b23275/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/reference_markers.hmm OceanDNA-b23275/protein.faa > /dev/null
[2023-03-19 00:33:48,020] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:48,020] [INFO] Found 6/6 markers.
[2023-03-19 00:33:48,068] [INFO] Query marker FASTA was written to OceanDNA-b23275/markers.fasta
[2023-03-19 00:33:48,072] [INFO] Task started: Blastn
[2023-03-19 00:33:48,072] [INFO] Running command: blastn -query OceanDNA-b23275/markers.fasta -db /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/reference_markers.fasta -out OceanDNA-b23275/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:48,969] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:48,972] [INFO] Selected 29 target genomes.
[2023-03-19 00:33:48,973] [INFO] Target genome list was writen to OceanDNA-b23275/target_genomes.txt
[2023-03-19 00:33:49,097] [INFO] Task started: fastANI
[2023-03-19 00:33:49,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg98dc31d9-b10c-457c-bbbb-62696a4f8bb9/OceanDNA-b23275.fa --refList OceanDNA-b23275/target_genomes.txt --output OceanDNA-b23275/fastani_result.tsv --threads 1
[2023-03-19 00:34:13,081] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:13,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:34:13,082] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:34:13,098] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:34:13,099] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:34:13,099] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	77.5399	336	1489	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.4635	294	1489	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.3897	308	1489	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.1774	374	1489	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.1594	480	1489	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.1304	485	1489	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.0078	306	1489	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.9102	269	1489	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.8883	250	1489	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.8456	212	1489	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8436	265	1489	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.8399	360	1489	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.7623	394	1489	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.6314	192	1489	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.6118	252	1489	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.6065	275	1489	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	76.5836	309	1489	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.5757	239	1489	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	76.5625	277	1489	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.5618	313	1489	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.4942	246	1489	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.4764	196	1489	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.3733	321	1489	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	76.3541	220	1489	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	76.2476	175	1489	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	76.1456	139	1489	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.1385	192	1489	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	76.1266	139	1489	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	76.0277	140	1489	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:34:13,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23275/tc_result.tsv
[2023-03-19 00:34:13,102] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:34:13,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:34:13,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/checkm_data
[2023-03-19 00:34:13,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:34:13,110] [INFO] Task started: CheckM
[2023-03-19 00:34:13,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23275/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23275/checkm_input OceanDNA-b23275/checkm_result
[2023-03-19 00:35:19,814] [INFO] Task succeeded: CheckM
[2023-03-19 00:35:19,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:35:19,821] [INFO] ===== Completeness check finished =====
[2023-03-19 00:35:19,821] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:35:19,821] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23275/markers.fasta)
[2023-03-19 00:35:19,822] [INFO] Task started: Blastn
[2023-03-19 00:35:19,823] [INFO] Running command: blastn -query OceanDNA-b23275/markers.fasta -db /var/lib/cwl/stg351e4258-4634-4dcb-a1f1-bef4e60c86e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23275/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:35:21,489] [INFO] Task succeeded: Blastn
[2023-03-19 00:35:21,492] [INFO] Selected 29 target genomes.
[2023-03-19 00:35:21,492] [INFO] Target genome list was writen to OceanDNA-b23275/target_genomes_gtdb.txt
[2023-03-19 00:35:21,513] [INFO] Task started: fastANI
[2023-03-19 00:35:21,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg98dc31d9-b10c-457c-bbbb-62696a4f8bb9/OceanDNA-b23275.fa --refList OceanDNA-b23275/target_genomes_gtdb.txt --output OceanDNA-b23275/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:35:46,520] [INFO] Task succeeded: fastANI
[2023-03-19 00:35:46,537] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:35:46,537] [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_009649675.1	s__HT1-32 sp009649675	78.0111	524	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__HT1-32;g__HT1-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	77.1525	483	1489	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_001603335.1	s__Alpha-05 sp001603335	77.1238	140	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	77.0773	280	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	77.0152	372	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	77.0078	372	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000315795.1	s__Caenispirillum salinarum	76.9107	270	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250275.1	s__Alpha-05 sp003250275	76.8805	183	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.8629	213	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.81	268	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_002195995.1	s__Inquilinus limosus_C	76.7942	399	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	76.7926	388	1489	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_003576685.1	s__SYSU-D60014 sp003576685	76.7835	258	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	76.782	258	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	76.7739	376	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356015.1	s__Azospirillum sp017356015	76.6925	329	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.6646	263	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884705.1	s__Reyranella sp005884705	76.6524	211	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	76.6348	199	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_016794005.1	s__Tagaea sp016794005	76.5933	195	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.5866	277	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	76.582	310	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	76.5471	279	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045115.1	s__Pseudaminobacter zhangyensis	76.516	216	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	76.4908	169	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792765.1	s__SBBV01 sp016792765	76.4364	258	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__SBBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	76.3339	238	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCA_009712185.1	s__Telmatospirillum sp009712185	76.2387	167	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	76.1151	140	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:35:46,540] [INFO] GTDB search result was written to OceanDNA-b23275/result_gtdb.tsv
[2023-03-19 00:35:46,543] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:35:46,548] [INFO] DFAST_QC result json was written to OceanDNA-b23275/dqc_result.json
[2023-03-19 00:35:46,548] [INFO] DFAST_QC completed!
[2023-03-19 00:35:46,548] [INFO] Total running time: 0h2m27s