[2023-03-15 17:19:45,546] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:19:45,548] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:19:45,549] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference
[2023-03-15 17:19:46,665] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:19:46,666] [INFO] Task started: Prodigal
[2023-03-15 17:19:46,666] [INFO] Running command: cat /var/lib/cwl/stg21e0daf0-67f5-455c-9c0b-b57b9bac120d/OceanDNA-b26840.fa | prodigal -d OceanDNA-b26840/cds.fna -a OceanDNA-b26840/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:19:59,152] [INFO] Task succeeded: Prodigal
[2023-03-15 17:19:59,152] [INFO] Task started: HMMsearch
[2023-03-15 17:19:59,153] [INFO] Running command: hmmsearch --tblout OceanDNA-b26840/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/reference_markers.hmm OceanDNA-b26840/protein.faa > /dev/null
[2023-03-15 17:19:59,341] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:19:59,341] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg21e0daf0-67f5-455c-9c0b-b57b9bac120d/OceanDNA-b26840.fa]
[2023-03-15 17:19:59,370] [INFO] Query marker FASTA was written to OceanDNA-b26840/markers.fasta
[2023-03-15 17:19:59,371] [INFO] Task started: Blastn
[2023-03-15 17:19:59,372] [INFO] Running command: blastn -query OceanDNA-b26840/markers.fasta -db /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/reference_markers.fasta -out OceanDNA-b26840/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:20:00,055] [INFO] Task succeeded: Blastn
[2023-03-15 17:20:00,060] [INFO] Selected 10 target genomes.
[2023-03-15 17:20:00,060] [INFO] Target genome list was writen to OceanDNA-b26840/target_genomes.txt
[2023-03-15 17:20:00,067] [INFO] Task started: fastANI
[2023-03-15 17:20:00,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e0daf0-67f5-455c-9c0b-b57b9bac120d/OceanDNA-b26840.fa --refList OceanDNA-b26840/target_genomes.txt --output OceanDNA-b26840/fastani_result.tsv --threads 1
[2023-03-15 17:20:08,843] [INFO] Task succeeded: fastANI
[2023-03-15 17:20:08,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:20:08,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:20:08,851] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:20:08,851] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:20:08,851] [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 alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	85.991	457	531	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.5544	385	531	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	82.5399	380	531	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.7593	303	531	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.6348	321	531	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.0729	186	531	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.9114	194	531	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.6939	163	531	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.4968	168	531	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	77.3773	154	531	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:20:08,853] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26840/tc_result.tsv
[2023-03-15 17:20:08,853] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:20:08,853] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:20:08,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/checkm_data
[2023-03-15 17:20:08,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:20:08,998] [INFO] Task started: CheckM
[2023-03-15 17:20:08,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26840/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26840/checkm_input OceanDNA-b26840/checkm_result
[2023-03-15 17:20:44,055] [INFO] Task succeeded: CheckM
[2023-03-15 17:20:44,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.57%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:20:44,075] [INFO] ===== Completeness check finished =====
[2023-03-15 17:20:44,075] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:20:44,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26840/markers.fasta)
[2023-03-15 17:20:44,076] [INFO] Task started: Blastn
[2023-03-15 17:20:44,076] [INFO] Running command: blastn -query OceanDNA-b26840/markers.fasta -db /var/lib/cwl/stg0fe826ec-01fc-4d70-bc9b-641733fd6483/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26840/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:20:45,226] [INFO] Task succeeded: Blastn
[2023-03-15 17:20:45,234] [INFO] Selected 10 target genomes.
[2023-03-15 17:20:45,234] [INFO] Target genome list was writen to OceanDNA-b26840/target_genomes_gtdb.txt
[2023-03-15 17:20:45,266] [INFO] Task started: fastANI
[2023-03-15 17:20:45,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg21e0daf0-67f5-455c-9c0b-b57b9bac120d/OceanDNA-b26840.fa --refList OceanDNA-b26840/target_genomes_gtdb.txt --output OceanDNA-b26840/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:20:53,601] [INFO] Task succeeded: fastANI
[2023-03-15 17:20:53,608] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:20:53,608] [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_018829385.1	s__Hoeflea sp018829385	94.4878	369	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	86.2203	461	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCA_002733955.1	s__Hoeflea sp002733955	84.2177	432	531	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	83.9671	440	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	82.9746	409	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_014359905.1	s__Hoeflea sp014359905	82.9093	401	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	82.5544	385	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	82.5247	381	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	82.1903	301	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	80.7812	303	531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:20:53,613] [INFO] GTDB search result was written to OceanDNA-b26840/result_gtdb.tsv
[2023-03-15 17:20:53,619] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:20:53,624] [INFO] DFAST_QC result json was written to OceanDNA-b26840/dqc_result.json
[2023-03-15 17:20:53,624] [INFO] DFAST_QC completed!
[2023-03-15 17:20:53,624] [INFO] Total running time: 0h1m8s