[2023-03-15 17:46:31,557] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,558] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,558] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference
[2023-03-15 17:46:32,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,673] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,673] [INFO] Running command: cat /var/lib/cwl/stg1763330d-f1bb-4f5a-ba5d-b62f5ee6fada/OceanDNA-b24172.fa | prodigal -d OceanDNA-b24172/cds.fna -a OceanDNA-b24172/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:47,320] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:47,321] [INFO] Task started: HMMsearch
[2023-03-15 17:46:47,321] [INFO] Running command: hmmsearch --tblout OceanDNA-b24172/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/reference_markers.hmm OceanDNA-b24172/protein.faa > /dev/null
[2023-03-15 17:46:47,558] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:47,559] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1763330d-f1bb-4f5a-ba5d-b62f5ee6fada/OceanDNA-b24172.fa]
[2023-03-15 17:46:47,591] [INFO] Query marker FASTA was written to OceanDNA-b24172/markers.fasta
[2023-03-15 17:46:47,592] [INFO] Task started: Blastn
[2023-03-15 17:46:47,592] [INFO] Running command: blastn -query OceanDNA-b24172/markers.fasta -db /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/reference_markers.fasta -out OceanDNA-b24172/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:48,282] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:48,286] [INFO] Selected 29 target genomes.
[2023-03-15 17:46:48,286] [INFO] Target genome list was writen to OceanDNA-b24172/target_genomes.txt
[2023-03-15 17:46:48,302] [INFO] Task started: fastANI
[2023-03-15 17:46:48,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg1763330d-f1bb-4f5a-ba5d-b62f5ee6fada/OceanDNA-b24172.fa --refList OceanDNA-b24172/target_genomes.txt --output OceanDNA-b24172/fastani_result.tsv --threads 1
[2023-03-15 17:47:12,152] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:12,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:12,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:12,167] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:12,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:47:12,167] [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
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.852	133	596	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.5672	117	596	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.3111	87	596	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	76.2838	87	596	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	76.2835	87	596	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.2741	149	596	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.1985	156	596	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.1323	77	596	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.0238	161	596	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.0195	160	596	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.9848	174	596	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.9447	103	596	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.8977	111	596	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.8139	135	596	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.7171	104	596	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	75.6937	68	596	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	75.6747	69	596	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	75.6482	92	596	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	75.6453	54	596	95	below_threshold
Bradyrhizobium symbiodeficiens	strain=85S1MB	GCA_002266465.2	1404367	1404367	type	True	75.59	99	596	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	75.5878	93	596	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.5621	134	596	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.5265	136	596	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	75.5194	113	596	95	below_threshold
Bradyrhizobium diversitatis	strain=CNPSo 4019	GCA_016031635.1	2755406	2755406	type	True	75.4858	107	596	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.4492	97	596	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:47:12,168] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24172/tc_result.tsv
[2023-03-15 17:47:12,168] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:12,168] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:12,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/checkm_data
[2023-03-15 17:47:12,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:12,174] [INFO] Task started: CheckM
[2023-03-15 17:47:12,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24172/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24172/checkm_input OceanDNA-b24172/checkm_result
[2023-03-15 17:47:50,257] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:50,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:50,269] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:50,269] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:50,269] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24172/markers.fasta)
[2023-03-15 17:47:50,270] [INFO] Task started: Blastn
[2023-03-15 17:47:50,270] [INFO] Running command: blastn -query OceanDNA-b24172/markers.fasta -db /var/lib/cwl/stgf5b9fcf1-5f04-488c-b301-65b2f8af585f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24172/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:51,347] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:51,349] [INFO] Selected 27 target genomes.
[2023-03-15 17:47:51,349] [INFO] Target genome list was writen to OceanDNA-b24172/target_genomes_gtdb.txt
[2023-03-15 17:47:51,408] [INFO] Task started: fastANI
[2023-03-15 17:47:51,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg1763330d-f1bb-4f5a-ba5d-b62f5ee6fada/OceanDNA-b24172.fa --refList OceanDNA-b24172/target_genomes_gtdb.txt --output OceanDNA-b24172/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:48:12,667] [INFO] Task succeeded: fastANI
[2023-03-15 17:48:12,681] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:48:12,681] [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_002924445.1	s__Minwuia thermotolerans	76.852	133	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Minwuiales;f__Minwuiaceae;g__Minwuia	95.0	97.67	95.35	0.91	0.86	3	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.8035	184	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307375.1	s__JAFKFH01 sp017307375	76.6412	163	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172325.1	s__Oceanibacterium hippocampi	76.5672	117	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sneathiellales;f__Sneathiellaceae;g__Oceanibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	76.2381	123	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCA_006739055.1	s__Stella vacuolata	76.2228	166	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.2161	179	596	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_002796975.1	s__Ferrovibrio sp002796975	76.187	114	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002195995.1	s__Inquilinus limosus_C	76.1519	159	596	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_002781745.1	s__UBA1479 sp002781745	76.1365	74	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	76.0677	119	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_001305595.1	s__Azospirillum thiophilum	76.0479	160	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003610575.1	s__Stappia sp003610575	76.0284	108	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	98.18	0.97	0.97	2	-
GCA_001939945.1	s__Aerophototrophica crusticola	76.0187	135	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Aerophototrophica	95.0	99.94	99.94	0.97	0.97	2	-
GCF_003572205.1	s__Algihabitans albus	75.9602	65	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Algihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	75.9436	73	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315795.1	s__Caenispirillum salinarum	75.8621	114	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	75.8338	72	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003015025.1	s__Nitratireductor_D sp003015025	75.7247	90	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	99.00	99.00	0.89	0.89	2	-
GCF_005160265.1	s__Phreatobacter sp005160265	75.7028	74	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	75.6629	111	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	75.6332	90	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCA_001556125.1	s__Bosea sp001556125	75.6143	85	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	96.92	96.82	0.82	0.77	9	-
GCF_001509835.1	s__Bosea sp001509835	75.6031	96	596	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 17:48:12,682] [INFO] GTDB search result was written to OceanDNA-b24172/result_gtdb.tsv
[2023-03-15 17:48:12,684] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:48:12,687] [INFO] DFAST_QC result json was written to OceanDNA-b24172/dqc_result.json
[2023-03-15 17:48:12,688] [INFO] DFAST_QC completed!
[2023-03-15 17:48:12,688] [INFO] Total running time: 0h1m41s