[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,867] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,534] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,534] [INFO] Running command: cat /var/lib/cwl/stgf6da6037-cd5d-4490-957f-5c28daa34427/OceanDNA-b36161.fa | prodigal -d OceanDNA-b36161/cds.fna -a OceanDNA-b36161/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:50,448] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:50,449] [INFO] Task started: HMMsearch
[2023-03-16 03:47:50,449] [INFO] Running command: hmmsearch --tblout OceanDNA-b36161/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/reference_markers.hmm OceanDNA-b36161/protein.faa > /dev/null
[2023-03-16 03:47:50,729] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:50,730] [INFO] Found 6/6 markers.
[2023-03-16 03:47:50,748] [INFO] Query marker FASTA was written to OceanDNA-b36161/markers.fasta
[2023-03-16 03:47:50,748] [INFO] Task started: Blastn
[2023-03-16 03:47:50,749] [INFO] Running command: blastn -query OceanDNA-b36161/markers.fasta -db /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/reference_markers.fasta -out OceanDNA-b36161/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:51,530] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:51,531] [INFO] Selected 20 target genomes.
[2023-03-16 03:47:51,531] [INFO] Target genome list was writen to OceanDNA-b36161/target_genomes.txt
[2023-03-16 03:47:51,543] [INFO] Task started: fastANI
[2023-03-16 03:47:51,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6da6037-cd5d-4490-957f-5c28daa34427/OceanDNA-b36161.fa --refList OceanDNA-b36161/target_genomes.txt --output OceanDNA-b36161/fastani_result.tsv --threads 1
[2023-03-16 03:48:04,709] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:04,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:04,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:04,719] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:04,720] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:04,720] [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 japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	82.6388	651	844	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	78.7296	331	844	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	78.689	317	844	95	below_threshold
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	78.2518	247	844	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	76.1692	78	844	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.0946	53	844	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	75.9452	63	844	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	75.9436	63	844	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	75.9436	63	844	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.9409	68	844	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.9301	78	844	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.8486	98	844	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	75.7055	62	844	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7029	62	844	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	75.6916	63	844	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	75.5668	59	844	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:04,720] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36161/tc_result.tsv
[2023-03-16 03:48:04,720] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:04,720] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:04,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/checkm_data
[2023-03-16 03:48:04,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:04,728] [INFO] Task started: CheckM
[2023-03-16 03:48:04,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36161/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36161/checkm_input OceanDNA-b36161/checkm_result
[2023-03-16 03:48:45,536] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:45,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.96%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:45,539] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:45,539] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:45,539] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36161/markers.fasta)
[2023-03-16 03:48:45,540] [INFO] Task started: Blastn
[2023-03-16 03:48:45,540] [INFO] Running command: blastn -query OceanDNA-b36161/markers.fasta -db /var/lib/cwl/stgfb54a7cf-c446-4680-ba65-f87a8c9fe5ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36161/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:46,953] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:46,954] [INFO] Selected 13 target genomes.
[2023-03-16 03:48:46,954] [INFO] Target genome list was writen to OceanDNA-b36161/target_genomes_gtdb.txt
[2023-03-16 03:48:47,034] [INFO] Task started: fastANI
[2023-03-16 03:48:47,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6da6037-cd5d-4490-957f-5c28daa34427/OceanDNA-b36161.fa --refList OceanDNA-b36161/target_genomes_gtdb.txt --output OceanDNA-b36161/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:56,172] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:56,179] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:48:56,179] [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_002320455.1	s__Salinisphaera sp002320455	99.8915	780	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003788585.1	s__Salinisphaera japonica	82.6806	649	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715985.1	s__Salinisphaera sp002715985	81.7818	446	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	-
GCF_003602005.1	s__Salinisphaera sp003602005	79.2926	411	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	79.1052	364	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	78.7536	329	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	78.6751	317	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	78.6445	372	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	75.9436	63	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_008312895.1	s__Luteimonas sp008312895	75.6749	66	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	75.5668	59	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:56,179] [INFO] GTDB search result was written to OceanDNA-b36161/result_gtdb.tsv
[2023-03-16 03:48:56,179] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:56,181] [INFO] DFAST_QC result json was written to OceanDNA-b36161/dqc_result.json
[2023-03-16 03:48:56,181] [INFO] DFAST_QC completed!
[2023-03-16 03:48:56,181] [INFO] Total running time: 0h1m23s