[2023-03-18 22:44:57,941] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,943] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,943] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference
[2023-03-18 22:44:59,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,094] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,094] [INFO] Running command: cat /var/lib/cwl/stgcf0e5e8b-6b74-44f0-ab35-31b2fc2242d7/OceanDNA-b26869.fa | prodigal -d OceanDNA-b26869/cds.fna -a OceanDNA-b26869/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:24,159] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:24,159] [INFO] Task started: HMMsearch
[2023-03-18 22:45:24,159] [INFO] Running command: hmmsearch --tblout OceanDNA-b26869/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/reference_markers.hmm OceanDNA-b26869/protein.faa > /dev/null
[2023-03-18 22:45:24,387] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:24,387] [INFO] Found 6/6 markers.
[2023-03-18 22:45:24,420] [INFO] Query marker FASTA was written to OceanDNA-b26869/markers.fasta
[2023-03-18 22:45:24,421] [INFO] Task started: Blastn
[2023-03-18 22:45:24,421] [INFO] Running command: blastn -query OceanDNA-b26869/markers.fasta -db /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/reference_markers.fasta -out OceanDNA-b26869/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:25,386] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:25,391] [INFO] Selected 24 target genomes.
[2023-03-18 22:45:25,391] [INFO] Target genome list was writen to OceanDNA-b26869/target_genomes.txt
[2023-03-18 22:45:25,406] [INFO] Task started: fastANI
[2023-03-18 22:45:25,407] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf0e5e8b-6b74-44f0-ab35-31b2fc2242d7/OceanDNA-b26869.fa --refList OceanDNA-b26869/target_genomes.txt --output OceanDNA-b26869/fastani_result.tsv --threads 1
[2023-03-18 22:45:46,682] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:46,682] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:46,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:46,696] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:46,696] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:45:46,696] [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
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	79.79	601	1361	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.1358	583	1361	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.6964	503	1361	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	78.6856	445	1361	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	78.5764	492	1361	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.4631	458	1361	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	78.4413	484	1361	95	below_threshold
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	78.3278	431	1361	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.2309	419	1361	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	78.1561	417	1361	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	78.0714	381	1361	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.9237	361	1361	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	77.8242	376	1361	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	77.7947	369	1361	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	77.7261	366	1361	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.6618	378	1361	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.6177	390	1361	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.5508	378	1361	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	77.4578	393	1361	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	76.0349	119	1361	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	75.9407	100	1361	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	75.893	96	1361	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	75.8867	95	1361	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	75.7984	93	1361	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:46,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26869/tc_result.tsv
[2023-03-18 22:45:46,714] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:46,714] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:46,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/checkm_data
[2023-03-18 22:45:46,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:46,846] [INFO] Task started: CheckM
[2023-03-18 22:45:46,847] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26869/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26869/checkm_input OceanDNA-b26869/checkm_result
[2023-03-18 22:46:47,730] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:47,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.68%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:48,078] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:48,078] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:48,078] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26869/markers.fasta)
[2023-03-18 22:46:48,079] [INFO] Task started: Blastn
[2023-03-18 22:46:48,079] [INFO] Running command: blastn -query OceanDNA-b26869/markers.fasta -db /var/lib/cwl/stgfcdf1258-c2c9-4ff7-b2e0-0b54c5a7b56d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26869/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:49,994] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:49,997] [INFO] Selected 17 target genomes.
[2023-03-18 22:46:49,997] [INFO] Target genome list was writen to OceanDNA-b26869/target_genomes_gtdb.txt
[2023-03-18 22:46:50,039] [INFO] Task started: fastANI
[2023-03-18 22:46:50,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf0e5e8b-6b74-44f0-ab35-31b2fc2242d7/OceanDNA-b26869.fa --refList OceanDNA-b26869/target_genomes_gtdb.txt --output OceanDNA-b26869/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:47:04,359] [INFO] Task succeeded: fastANI
[2023-03-18 22:47:04,369] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:47:04,370] [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_002709005.1	s__Pseudohoeflea sp002709005	99.7606	1173	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004354915.1	s__Pseudohoeflea suaedae	83.469	871	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707605.1	s__Pseudohoeflea sp002707605	82.8841	908	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	98.85	97.79	0.96	0.89	4	-
GCF_001703635.1	s__Hoeflea olei	79.8029	599	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	79.6983	589	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182275.1	s__Hoeflea marina	79.1358	583	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	78.894	336	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	78.3032	437	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
GCF_900220985.1	s__Hoeflea halophila	78.1424	417	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	77.8183	385	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_014851675.1	s__Mycoplana sp014851675	77.7681	323	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688075.1	s__Mesorhizobium sp000688075	77.5853	388	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	76.331	137	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	75.9226	115	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_003056335.1	s__Paracoccus indicus	75.8867	95	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111675.1	s__Paracoccus homiensis	75.7984	93	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002294185.1	s__Paracoccus sp002294185	75.6592	104	1361	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-18 22:47:04,372] [INFO] GTDB search result was written to OceanDNA-b26869/result_gtdb.tsv
[2023-03-18 22:47:04,372] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:47:04,376] [INFO] DFAST_QC result json was written to OceanDNA-b26869/dqc_result.json
[2023-03-18 22:47:04,376] [INFO] DFAST_QC completed!
[2023-03-18 22:47:04,376] [INFO] Total running time: 0h2m6s