[2023-03-19 00:01:03,442] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,442] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference
[2023-03-19 00:01:04,684] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,684] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,684] [INFO] Running command: cat /var/lib/cwl/stg51325a6e-13ba-4cd5-b044-90340e2b7c7d/OceanDNA-b26837.fa | prodigal -d OceanDNA-b26837/cds.fna -a OceanDNA-b26837/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:20,212] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:20,212] [INFO] Task started: HMMsearch
[2023-03-19 00:01:20,212] [INFO] Running command: hmmsearch --tblout OceanDNA-b26837/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/reference_markers.hmm OceanDNA-b26837/protein.faa > /dev/null
[2023-03-19 00:01:20,435] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:20,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51325a6e-13ba-4cd5-b044-90340e2b7c7d/OceanDNA-b26837.fa]
[2023-03-19 00:01:20,461] [INFO] Query marker FASTA was written to OceanDNA-b26837/markers.fasta
[2023-03-19 00:01:20,461] [INFO] Task started: Blastn
[2023-03-19 00:01:20,461] [INFO] Running command: blastn -query OceanDNA-b26837/markers.fasta -db /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/reference_markers.fasta -out OceanDNA-b26837/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:21,045] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:21,046] [INFO] Selected 11 target genomes.
[2023-03-19 00:01:21,046] [INFO] Target genome list was writen to OceanDNA-b26837/target_genomes.txt
[2023-03-19 00:01:21,051] [INFO] Task started: fastANI
[2023-03-19 00:01:21,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg51325a6e-13ba-4cd5-b044-90340e2b7c7d/OceanDNA-b26837.fa --refList OceanDNA-b26837/target_genomes.txt --output OceanDNA-b26837/fastani_result.tsv --threads 1
[2023-03-19 00:01:30,250] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:30,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:30,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:30,258] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:30,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:30,258] [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	86.0804	655	760	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	82.5262	549	760	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	82.1921	527	760	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.5702	437	760	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.9376	426	760	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0855	258	760	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.9616	225	760	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	77.8107	248	760	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.7992	225	760	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	77.712	202	760	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	77.3981	173	760	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:30,258] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26837/tc_result.tsv
[2023-03-19 00:01:30,258] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:30,258] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:30,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/checkm_data
[2023-03-19 00:01:30,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:30,264] [INFO] Task started: CheckM
[2023-03-19 00:01:30,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26837/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26837/checkm_input OceanDNA-b26837/checkm_result
[2023-03-19 00:02:11,730] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:11,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.25%
Contamintation: 16.67%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:11,734] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:11,734] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:11,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26837/markers.fasta)
[2023-03-19 00:02:11,734] [INFO] Task started: Blastn
[2023-03-19 00:02:11,734] [INFO] Running command: blastn -query OceanDNA-b26837/markers.fasta -db /var/lib/cwl/stg90ccc7fa-5e1a-4c11-a430-6185a88f8f5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26837/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:12,535] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:12,535] [INFO] Selected 10 target genomes.
[2023-03-19 00:02:12,536] [INFO] Target genome list was writen to OceanDNA-b26837/target_genomes_gtdb.txt
[2023-03-19 00:02:12,563] [INFO] Task started: fastANI
[2023-03-19 00:02:12,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg51325a6e-13ba-4cd5-b044-90340e2b7c7d/OceanDNA-b26837.fa --refList OceanDNA-b26837/target_genomes_gtdb.txt --output OceanDNA-b26837/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:21,206] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:21,213] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:02:21,213] [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	90.8852	499	760	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	85.7989	642	760	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	83.7221	609	760	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	83.2534	579	760	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	83.016	560	760	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	82.946	576	760	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_900220985.1	s__Hoeflea halophila	82.5262	549	760	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	82.3429	385	760	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	82.1919	527	760	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	80.5702	437	760	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:21,213] [INFO] GTDB search result was written to OceanDNA-b26837/result_gtdb.tsv
[2023-03-19 00:02:21,213] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:21,214] [INFO] DFAST_QC result json was written to OceanDNA-b26837/dqc_result.json
[2023-03-19 00:02:21,215] [INFO] DFAST_QC completed!
[2023-03-19 00:02:21,215] [INFO] Total running time: 0h1m18s