[2023-03-16 18:07:24,887] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:07:24,887] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:07:24,887] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference
[2023-03-16 18:07:25,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:07:25,964] [INFO] Task started: Prodigal
[2023-03-16 18:07:25,964] [INFO] Running command: cat /var/lib/cwl/stg3e2d6450-fc02-4526-93ab-45e316739500/OceanDNA-b23308.fa | prodigal -d OceanDNA-b23308/cds.fna -a OceanDNA-b23308/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:07:43,627] [INFO] Task succeeded: Prodigal
[2023-03-16 18:07:43,627] [INFO] Task started: HMMsearch
[2023-03-16 18:07:43,627] [INFO] Running command: hmmsearch --tblout OceanDNA-b23308/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/reference_markers.hmm OceanDNA-b23308/protein.faa > /dev/null
[2023-03-16 18:07:43,988] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:07:43,988] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e2d6450-fc02-4526-93ab-45e316739500/OceanDNA-b23308.fa]
[2023-03-16 18:07:44,015] [INFO] Query marker FASTA was written to OceanDNA-b23308/markers.fasta
[2023-03-16 18:07:44,017] [INFO] Task started: Blastn
[2023-03-16 18:07:44,017] [INFO] Running command: blastn -query OceanDNA-b23308/markers.fasta -db /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/reference_markers.fasta -out OceanDNA-b23308/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:07:44,743] [INFO] Task succeeded: Blastn
[2023-03-16 18:07:44,744] [INFO] Selected 30 target genomes.
[2023-03-16 18:07:44,744] [INFO] Target genome list was writen to OceanDNA-b23308/target_genomes.txt
[2023-03-16 18:07:44,801] [INFO] Task started: fastANI
[2023-03-16 18:07:44,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2d6450-fc02-4526-93ab-45e316739500/OceanDNA-b23308.fa --refList OceanDNA-b23308/target_genomes.txt --output OceanDNA-b23308/fastani_result.tsv --threads 1
[2023-03-16 18:08:18,107] [INFO] Task succeeded: fastANI
[2023-03-16 18:08:18,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:08:18,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:08:18,119] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:08:18,120] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:08:18,120] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.1335	71	580	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.8547	54	580	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	75.7702	68	580	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.7251	89	580	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.6824	61	580	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.6768	90	580	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.6364	58	580	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	75.6302	77	580	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.6292	60	580	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.6166	61	580	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.6005	81	580	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.5462	84	580	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4426	94	580	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4315	95	580	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.4242	81	580	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	75.4137	85	580	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.354	66	580	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.2777	59	580	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.2527	83	580	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:08:18,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23308/tc_result.tsv
[2023-03-16 18:08:18,120] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:08:18,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:08:18,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/checkm_data
[2023-03-16 18:08:18,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:08:18,226] [INFO] Task started: CheckM
[2023-03-16 18:08:18,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23308/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23308/checkm_input OceanDNA-b23308/checkm_result
[2023-03-16 18:09:04,559] [INFO] Task succeeded: CheckM
[2023-03-16 18:09:04,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.11%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 18:09:04,562] [INFO] ===== Completeness check finished =====
[2023-03-16 18:09:04,562] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:09:04,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23308/markers.fasta)
[2023-03-16 18:09:04,563] [INFO] Task started: Blastn
[2023-03-16 18:09:04,563] [INFO] Running command: blastn -query OceanDNA-b23308/markers.fasta -db /var/lib/cwl/stgb7591781-10c8-42a7-b5d5-06714599e826/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23308/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:05,634] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:05,635] [INFO] Selected 33 target genomes.
[2023-03-16 18:09:05,635] [INFO] Target genome list was writen to OceanDNA-b23308/target_genomes_gtdb.txt
[2023-03-16 18:09:05,679] [INFO] Task started: fastANI
[2023-03-16 18:09:05,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2d6450-fc02-4526-93ab-45e316739500/OceanDNA-b23308.fa --refList OceanDNA-b23308/target_genomes_gtdb.txt --output OceanDNA-b23308/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:31,125] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:31,137] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:09:31,137] [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
GCF_001618175.1	s__Oceanibaculum pacificum	76.1562	70	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.8584	83	580	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_017876155.1	s__Azospirillum rugosum	75.7251	89	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	75.6611	62	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	75.6443	61	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	75.6364	58	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCA_009377375.1	s__WHUE01 sp009377375	75.6259	63	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	75.6258	75	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	75.6153	66	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002195995.1	s__Inquilinus limosus_C	75.6124	81	580	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_003233655.1	s__Azospirillum ramasamyi	75.6123	80	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	75.5978	89	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	75.5588	78	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423185.1	s__Inquilinus limosus	75.5567	83	580	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_006738645.1	s__Stella humosa	75.4423	94	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429625.1	s__Azospirillum halopraeferens	75.4344	75	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	75.3773	52	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.3485	54	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840595.1	s__Bin65 sp009840595	75.3461	51	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
GCA_017307955.1	s__Kaistia sp017307955	75.3357	51	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	75.2777	59	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793045.1	s__JAEUKZ01 sp016793045	75.2058	63	580	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JAEUKZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:31,138] [INFO] GTDB search result was written to OceanDNA-b23308/result_gtdb.tsv
[2023-03-16 18:09:31,138] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:31,140] [INFO] DFAST_QC result json was written to OceanDNA-b23308/dqc_result.json
[2023-03-16 18:09:31,140] [INFO] DFAST_QC completed!
[2023-03-16 18:09:31,140] [INFO] Total running time: 0h2m6s