[2023-03-15 07:49:00,146] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:49:00,150] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:49:00,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference
[2023-03-15 07:49:01,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:49:01,266] [INFO] Task started: Prodigal
[2023-03-15 07:49:01,266] [INFO] Running command: cat /var/lib/cwl/stg0301134d-7346-4b43-a11f-6358ddc4f09e/OceanDNA-b36071.fa | prodigal -d OceanDNA-b36071/cds.fna -a OceanDNA-b36071/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:49:20,687] [INFO] Task succeeded: Prodigal
[2023-03-15 07:49:20,687] [INFO] Task started: HMMsearch
[2023-03-15 07:49:20,687] [INFO] Running command: hmmsearch --tblout OceanDNA-b36071/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/reference_markers.hmm OceanDNA-b36071/protein.faa > /dev/null
[2023-03-15 07:49:20,892] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:49:20,893] [INFO] Found 6/6 markers.
[2023-03-15 07:49:20,957] [INFO] Query marker FASTA was written to OceanDNA-b36071/markers.fasta
[2023-03-15 07:49:20,958] [INFO] Task started: Blastn
[2023-03-15 07:49:20,959] [INFO] Running command: blastn -query OceanDNA-b36071/markers.fasta -db /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/reference_markers.fasta -out OceanDNA-b36071/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:49:21,785] [INFO] Task succeeded: Blastn
[2023-03-15 07:49:21,792] [INFO] Selected 30 target genomes.
[2023-03-15 07:49:21,793] [INFO] Target genome list was writen to OceanDNA-b36071/target_genomes.txt
[2023-03-15 07:49:21,808] [INFO] Task started: fastANI
[2023-03-15 07:49:21,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg0301134d-7346-4b43-a11f-6358ddc4f09e/OceanDNA-b36071.fa --refList OceanDNA-b36071/target_genomes.txt --output OceanDNA-b36071/fastani_result.tsv --threads 1
[2023-03-15 07:49:39,268] [INFO] Task succeeded: fastANI
[2023-03-15 07:49:39,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:49:39,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:49:39,284] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:49:39,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:49:39,284] [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
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	76.6971	76	993	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.6025	111	993	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	76.5655	60	993	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	76.5386	122	993	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	76.4958	156	993	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	76.4351	77	993	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.4334	79	993	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	76.3805	77	993	95	below_threshold
Abyssibacter profundi	strain=OUC007	GCA_003151135.1	2182787	2182787	type	True	76.3801	74	993	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2803	84	993	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.2181	119	993	95	below_threshold
Oceanococcus atlanticus	strain=22II-S10r2	GCA_002088235.1	1317117	1317117	type	True	76.2092	110	993	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.1972	107	993	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.1853	79	993	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	76.1547	64	993	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	76.1432	58	993	95	below_threshold
Lysobacter penaei	strain=SG-8	GCA_014145395.1	2759900	2759900	type	True	76.1167	63	993	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.0905	61	993	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	76.0862	75	993	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	76.0704	90	993	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.0437	63	993	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.8221	69	993	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	75.809	52	993	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7536	59	993	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.7111	63	993	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	75.6952	52	993	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.6681	51	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:49:39,288] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36071/tc_result.tsv
[2023-03-15 07:49:39,290] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:49:39,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:49:39,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/checkm_data
[2023-03-15 07:49:39,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:49:39,297] [INFO] Task started: CheckM
[2023-03-15 07:49:39,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36071/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36071/checkm_input OceanDNA-b36071/checkm_result
[2023-03-15 07:50:29,075] [INFO] Task succeeded: CheckM
[2023-03-15 07:50:29,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:50:29,185] [INFO] ===== Completeness check finished =====
[2023-03-15 07:50:29,185] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:50:29,185] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36071/markers.fasta)
[2023-03-15 07:50:29,186] [INFO] Task started: Blastn
[2023-03-15 07:50:29,186] [INFO] Running command: blastn -query OceanDNA-b36071/markers.fasta -db /var/lib/cwl/stg02a2f564-5c42-4b04-abb6-5d068cb4f533/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36071/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:50:30,749] [INFO] Task succeeded: Blastn
[2023-03-15 07:50:30,769] [INFO] Selected 32 target genomes.
[2023-03-15 07:50:30,769] [INFO] Target genome list was writen to OceanDNA-b36071/target_genomes_gtdb.txt
[2023-03-15 07:50:30,847] [INFO] Task started: fastANI
[2023-03-15 07:50:30,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg0301134d-7346-4b43-a11f-6358ddc4f09e/OceanDNA-b36071.fa --refList OceanDNA-b36071/target_genomes_gtdb.txt --output OceanDNA-b36071/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:50:47,177] [INFO] Task succeeded: fastANI
[2023-03-15 07:50:47,192] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:50:47,192] [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_014762505.1	s__SpSt-1174 sp014762505	76.9168	92	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683405.1	s__GCA-2683405 sp002683405	76.5434	89	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__GCA-2683405	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711955.1	s__Nevskia soli	76.5386	122	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565775.1	s__SKGQ01 sp003565775	76.5368	64	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__SKGQ01	95.0	99.57	99.57	0.95	0.95	2	-
GCF_002930645.1	s__Solimonas_A fluminis	76.4824	156	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	76.4334	79	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.385	90	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_003151135.1	s__Abyssibacter profundi	76.3801	74	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__Abyssibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCA_011321775.1	s__Thiogranum sp011321775	76.3736	60	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377205.1	s__Thioalkalivibrio sp000377205	76.3493	67	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	99.40	99.38	0.97	0.97	3	-
GCF_003177035.1	s__Salinisphaera sp003177035	76.3204	74	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017744135.1	s__Salinisphaera sp017744135	76.2974	96	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.2925	81	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.2757	83	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822975.1	s__Nevskia sp903822975	76.2548	84	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000754095.2	s__Acidihalobacter prosperus	76.226	62	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	76.1782	63	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	76.1689	57	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272825.1	s__GCA-2722315 sp012272825	76.1117	72	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664325.1	s__Alkalilimnicola mobilis	76.0901	59	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola	95.0	98.61	98.57	0.90	0.85	3	-
GCF_011058255.1	s__XN24 sp011058255	76.0408	74	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320455.1	s__Salinisphaera sp002320455	76.0354	55	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	75.9356	73	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_011089885.1	s__XN24 sp011089885	75.8673	75	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240695.1	s__Pseudoxanthomonas_B suwonensis_A	75.7268	64	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149435.1	s__E85 sp003149435	75.6719	69	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002782905.1	s__GCA-002840015 sp002782905	75.3668	51	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__GCA-002840015	95.0	99.68	99.68	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:50:47,196] [INFO] GTDB search result was written to OceanDNA-b36071/result_gtdb.tsv
[2023-03-15 07:50:47,206] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:50:47,215] [INFO] DFAST_QC result json was written to OceanDNA-b36071/dqc_result.json
[2023-03-15 07:50:47,215] [INFO] DFAST_QC completed!
[2023-03-15 07:50:47,215] [INFO] Total running time: 0h1m47s