[2023-03-16 04:05:20,414] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,415] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference
[2023-03-16 04:05:22,127] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,128] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,128] [INFO] Running command: cat /var/lib/cwl/stgeda2c3ac-0ed7-4f51-a6b1-29d34b116e0f/OceanDNA-b33394.fa | prodigal -d OceanDNA-b33394/cds.fna -a OceanDNA-b33394/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:33,444] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:33,444] [INFO] Task started: HMMsearch
[2023-03-16 04:05:33,444] [INFO] Running command: hmmsearch --tblout OceanDNA-b33394/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/reference_markers.hmm OceanDNA-b33394/protein.faa > /dev/null
[2023-03-16 04:05:33,631] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:33,632] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeda2c3ac-0ed7-4f51-a6b1-29d34b116e0f/OceanDNA-b33394.fa]
[2023-03-16 04:05:33,655] [INFO] Query marker FASTA was written to OceanDNA-b33394/markers.fasta
[2023-03-16 04:05:33,655] [INFO] Task started: Blastn
[2023-03-16 04:05:33,656] [INFO] Running command: blastn -query OceanDNA-b33394/markers.fasta -db /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/reference_markers.fasta -out OceanDNA-b33394/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:34,422] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:34,423] [INFO] Selected 26 target genomes.
[2023-03-16 04:05:34,423] [INFO] Target genome list was writen to OceanDNA-b33394/target_genomes.txt
[2023-03-16 04:05:34,435] [INFO] Task started: fastANI
[2023-03-16 04:05:34,435] [INFO] Running command: fastANI --query /var/lib/cwl/stgeda2c3ac-0ed7-4f51-a6b1-29d34b116e0f/OceanDNA-b33394.fa --refList OceanDNA-b33394/target_genomes.txt --output OceanDNA-b33394/fastani_result.tsv --threads 1
[2023-03-16 04:05:52,293] [INFO] Task succeeded: fastANI
[2023-03-16 04:05:52,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:05:52,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:05:52,308] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:05:52,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:05:52,308] [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
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	85.2549	177	318	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	80.971	131	318	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	80.5195	137	318	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	80.1039	118	318	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.9721	112	318	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	79.8478	109	318	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.7843	116	318	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	79.6334	106	318	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.5906	105	318	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	79.5636	108	318	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.5603	113	318	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	79.4947	90	318	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	79.442	125	318	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	79.4221	106	318	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	79.4081	83	318	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	79.3744	97	318	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.3462	85	318	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.3385	99	318	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.3016	108	318	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.2865	116	318	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.2841	74	318	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.1207	101	318	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	78.9197	91	318	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.8541	80	318	95	below_threshold
Caenimonas koreensis	strain=EMB320	GCA_009646335.1	367474	367474	type	True	78.5778	84	318	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.0072	74	318	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:05:52,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33394/tc_result.tsv
[2023-03-16 04:05:52,308] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:05:52,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:05:52,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/checkm_data
[2023-03-16 04:05:52,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:05:52,314] [INFO] Task started: CheckM
[2023-03-16 04:05:52,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33394/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33394/checkm_input OceanDNA-b33394/checkm_result
[2023-03-16 04:06:24,787] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:24,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.70%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:24,790] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:24,790] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:24,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33394/markers.fasta)
[2023-03-16 04:06:24,790] [INFO] Task started: Blastn
[2023-03-16 04:06:24,790] [INFO] Running command: blastn -query OceanDNA-b33394/markers.fasta -db /var/lib/cwl/stgbd1d808b-46e3-45cc-be7a-cabc11d0defe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33394/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:06:26,252] [INFO] Task succeeded: Blastn
[2023-03-16 04:06:26,253] [INFO] Selected 9 target genomes.
[2023-03-16 04:06:26,253] [INFO] Target genome list was writen to OceanDNA-b33394/target_genomes_gtdb.txt
[2023-03-16 04:06:26,261] [INFO] Task started: fastANI
[2023-03-16 04:06:26,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgeda2c3ac-0ed7-4f51-a6b1-29d34b116e0f/OceanDNA-b33394.fa --refList OceanDNA-b33394/target_genomes_gtdb.txt --output OceanDNA-b33394/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:06:32,451] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:32,457] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:06:32,457] [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_013824015.1	s__Polaromonas sp013824015	88.823	164	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817205.1	s__Polaromonas sp013817205	86.3055	163	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379095.1	s__Polaromonas sp002379095	85.7436	194	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379085.1	s__Polaromonas sp002379085	85.5191	197	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641715.1	s__Polaromonas eurypsychrophila	85.2549	177	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002278925.1	s__Polaromonas sp002278925	84.6782	179	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	99.99	99.98	0.99	0.99	5	-
GCF_002001015.1	s__Polaromonas sp002001015	82.685	157	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103405.1	s__Polaromonas sp900103405	82.325	148	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	79.3548	119	318	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:06:32,457] [INFO] GTDB search result was written to OceanDNA-b33394/result_gtdb.tsv
[2023-03-16 04:06:32,458] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:06:32,459] [INFO] DFAST_QC result json was written to OceanDNA-b33394/dqc_result.json
[2023-03-16 04:06:32,460] [INFO] DFAST_QC completed!
[2023-03-16 04:06:32,460] [INFO] Total running time: 0h1m12s