[2023-03-18 02:53:05,582] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:53:05,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:53:05,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference
[2023-03-18 02:53:07,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:53:07,196] [INFO] Task started: Prodigal
[2023-03-18 02:53:07,196] [INFO] Running command: cat /var/lib/cwl/stg0e0d2d90-7b90-4c0a-b8b3-9c61ab6a9a13/OceanDNA-b33378.fa | prodigal -d OceanDNA-b33378/cds.fna -a OceanDNA-b33378/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:53:17,883] [INFO] Task succeeded: Prodigal
[2023-03-18 02:53:17,884] [INFO] Task started: HMMsearch
[2023-03-18 02:53:17,884] [INFO] Running command: hmmsearch --tblout OceanDNA-b33378/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/reference_markers.hmm OceanDNA-b33378/protein.faa > /dev/null
[2023-03-18 02:53:18,078] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:53:18,079] [INFO] Found 6/6 markers.
[2023-03-18 02:53:18,095] [INFO] Query marker FASTA was written to OceanDNA-b33378/markers.fasta
[2023-03-18 02:53:18,095] [INFO] Task started: Blastn
[2023-03-18 02:53:18,095] [INFO] Running command: blastn -query OceanDNA-b33378/markers.fasta -db /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/reference_markers.fasta -out OceanDNA-b33378/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:53:18,788] [INFO] Task succeeded: Blastn
[2023-03-18 02:53:18,788] [INFO] Selected 32 target genomes.
[2023-03-18 02:53:18,789] [INFO] Target genome list was writen to OceanDNA-b33378/target_genomes.txt
[2023-03-18 02:53:18,806] [INFO] Task started: fastANI
[2023-03-18 02:53:18,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0d2d90-7b90-4c0a-b8b3-9c61ab6a9a13/OceanDNA-b33378.fa --refList OceanDNA-b33378/target_genomes.txt --output OceanDNA-b33378/fastani_result.tsv --threads 1
[2023-03-18 02:53:36,369] [INFO] Task succeeded: fastANI
[2023-03-18 02:53:36,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:53:36,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:53:36,381] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:53:36,381] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:53:36,381] [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
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.722	101	436	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.5762	101	436	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.3891	85	436	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.3588	86	436	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	77.1501	70	436	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	76.917	55	436	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	76.917	55	436	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8208	65	436	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.7905	53	436	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	76.7742	65	436	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	76.6912	70	436	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	76.6543	62	436	95	below_threshold
Serpentinimonas raichei	strain=A1	GCA_000828895.1	1458425	1458425	type	True	76.649	51	436	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	76.6468	56	436	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	76.5809	52	436	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	76.559	58	436	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	76.5567	57	436	95	below_threshold
Caenimonas koreensis	strain=EMB320	GCA_009646335.1	367474	367474	type	True	76.5501	50	436	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	76.4573	56	436	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	76.4045	56	436	95	below_threshold
Polaromonas vacuolata	strain=KCTC 22033	GCA_012584515.1	37448	37448	type	True	76.3462	53	436	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:53:36,381] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33378/tc_result.tsv
[2023-03-18 02:53:36,381] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:53:36,382] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:53:36,382] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/checkm_data
[2023-03-18 02:53:36,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:53:36,386] [INFO] Task started: CheckM
[2023-03-18 02:53:36,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33378/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33378/checkm_input OceanDNA-b33378/checkm_result
[2023-03-18 02:54:07,803] [INFO] Task succeeded: CheckM
[2023-03-18 02:54:07,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.07%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:54:07,805] [INFO] ===== Completeness check finished =====
[2023-03-18 02:54:07,806] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:54:07,806] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33378/markers.fasta)
[2023-03-18 02:54:07,806] [INFO] Task started: Blastn
[2023-03-18 02:54:07,806] [INFO] Running command: blastn -query OceanDNA-b33378/markers.fasta -db /var/lib/cwl/stg2aa674eb-231d-441c-8c28-cc329ece4ede/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33378/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:54:09,082] [INFO] Task succeeded: Blastn
[2023-03-18 02:54:09,083] [INFO] Selected 29 target genomes.
[2023-03-18 02:54:09,083] [INFO] Target genome list was writen to OceanDNA-b33378/target_genomes_gtdb.txt
[2023-03-18 02:54:09,251] [INFO] Task started: fastANI
[2023-03-18 02:54:09,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e0d2d90-7b90-4c0a-b8b3-9c61ab6a9a13/OceanDNA-b33378.fa --refList OceanDNA-b33378/target_genomes_gtdb.txt --output OceanDNA-b33378/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:54:23,469] [INFO] Task succeeded: fastANI
[2023-03-18 02:54:23,484] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:54:23,484] [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_005789825.1	s__Limnohabitans sp005789825	84.1258	310	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	96.68	96.68	0.84	0.84	2	-
GCA_903887325.1	s__Limnohabitans sp903887325	82.9559	260	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.65	99.44	0.91	0.87	5	-
GCA_009925585.1	s__Limnohabitans sp009925585	81.7952	306	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.01	99.01	0.84	0.84	2	-
GCA_009693225.1	s__Limnohabitans sp009693225	80.959	189	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	78.9571	182	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063575.1	s__Limnohabitans_A sp003063575	77.85	93	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009921465.1	s__Limnohabitans sp009921465	77.6256	58	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903880855.1	s__Limnohabitans sp903880855	77.5617	76	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.14	98.09	0.92	0.91	4	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	77.5243	96	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063545.1	s__Limnohabitans sp003063545	77.4858	82	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778285.1	s__Limnohabitans_A sp002778285	77.4794	106	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969975.1	s__Limnohabitans sp018969975	77.4708	57	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063455.1	s__Limnohabitans_A parvus	77.3891	85	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778315.1	s__Limnohabitans sp002778315	77.3554	118	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.08	98.08	0.92	0.92	2	-
GCA_002256145.1	s__Limnohabitans_A sp002256145	77.3441	101	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778325.1	s__Limnohabitans sp002778325	77.3111	103	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886485.1	s__Limnohabitans sp903886485	77.2859	94	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCF_001269385.1	s__Limnohabitans_A sp001269385	77.1384	107	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903952885.1	s__Limnohabitans sp903952885	77.0973	59	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCA_009693505.1	s__Limnohabitans_A sp009693505	77.0719	75	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928635.1	s__Rhodoferax sp903928635	77.0523	72	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.42	99.41	0.86	0.86	3	-
GCA_009927195.1	s__Limnohabitans sp009927195	76.9397	67	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463455.1	s__Rhodoferax sp016463455	76.6413	61	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003417535.1	s__Hydrogenophaga borbori	76.5809	52	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.89	96.31	0.93	0.91	7	-
GCA_002842205.1	s__PHCI01 sp002842205	76.4955	74	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PHCI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428665.1	s__Acidovorax sp001428665	76.2869	54	436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.34	97.34	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 02:54:23,484] [INFO] GTDB search result was written to OceanDNA-b33378/result_gtdb.tsv
[2023-03-18 02:54:23,484] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:54:23,487] [INFO] DFAST_QC result json was written to OceanDNA-b33378/dqc_result.json
[2023-03-18 02:54:23,487] [INFO] DFAST_QC completed!
[2023-03-18 02:54:23,487] [INFO] Total running time: 0h1m18s