[2023-03-14 11:13:58,984] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:13:58,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:13:58,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference
[2023-03-14 11:14:00,598] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:00,598] [INFO] Task started: Prodigal
[2023-03-14 11:14:00,599] [INFO] Running command: cat /var/lib/cwl/stg7c5dded2-b71e-4ed4-8285-f0bb72422a66/OceanDNA-b24797.fa | prodigal -d OceanDNA-b24797/cds.fna -a OceanDNA-b24797/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:18,826] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:18,826] [INFO] Task started: HMMsearch
[2023-03-14 11:14:18,826] [INFO] Running command: hmmsearch --tblout OceanDNA-b24797/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/reference_markers.hmm OceanDNA-b24797/protein.faa > /dev/null
[2023-03-14 11:14:19,004] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:19,004] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7c5dded2-b71e-4ed4-8285-f0bb72422a66/OceanDNA-b24797.fa]
[2023-03-14 11:14:19,027] [INFO] Query marker FASTA was written to OceanDNA-b24797/markers.fasta
[2023-03-14 11:14:19,027] [INFO] Task started: Blastn
[2023-03-14 11:14:19,027] [INFO] Running command: blastn -query OceanDNA-b24797/markers.fasta -db /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/reference_markers.fasta -out OceanDNA-b24797/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:19,469] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:19,527] [INFO] Selected 11 target genomes.
[2023-03-14 11:14:19,527] [INFO] Target genome list was writen to OceanDNA-b24797/target_genomes.txt
[2023-03-14 11:14:19,536] [INFO] Task started: fastANI
[2023-03-14 11:14:19,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5dded2-b71e-4ed4-8285-f0bb72422a66/OceanDNA-b24797.fa --refList OceanDNA-b24797/target_genomes.txt --output OceanDNA-b24797/fastani_result.tsv --threads 1
[2023-03-14 11:14:28,286] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:28,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:28,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:28,294] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:28,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:28,294] [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
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	89.1656	879	977	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	88.6843	854	977	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	80.5484	602	977	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	80.4684	595	977	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.3725	65	977	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.9061	62	977	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.7664	90	977	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	75.5815	69	977	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.4221	67	977	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:28,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24797/tc_result.tsv
[2023-03-14 11:14:28,295] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:28,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:28,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/checkm_data
[2023-03-14 11:14:28,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:28,300] [INFO] Task started: CheckM
[2023-03-14 11:14:28,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24797/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24797/checkm_input OceanDNA-b24797/checkm_result
[2023-03-14 11:15:15,516] [INFO] Task succeeded: CheckM
[2023-03-14 11:15:15,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.02%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:15:15,519] [INFO] ===== Completeness check finished =====
[2023-03-14 11:15:15,519] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:15:15,520] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24797/markers.fasta)
[2023-03-14 11:15:15,520] [INFO] Task started: Blastn
[2023-03-14 11:15:15,520] [INFO] Running command: blastn -query OceanDNA-b24797/markers.fasta -db /var/lib/cwl/stg4a48dc34-12b1-4887-8f89-a96a1254c2c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24797/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:15:15,987] [INFO] Task succeeded: Blastn
[2023-03-14 11:15:15,988] [INFO] Selected 7 target genomes.
[2023-03-14 11:15:15,988] [INFO] Target genome list was writen to OceanDNA-b24797/target_genomes_gtdb.txt
[2023-03-14 11:15:15,996] [INFO] Task started: fastANI
[2023-03-14 11:15:15,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c5dded2-b71e-4ed4-8285-f0bb72422a66/OceanDNA-b24797.fa --refList OceanDNA-b24797/target_genomes_gtdb.txt --output OceanDNA-b24797/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:15:22,978] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:22,982] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:15:22,982] [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
GCF_014904795.1	s__Nisaea nitritireducens	89.1656	879	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	88.6843	854	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	80.4654	596	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	80.4055	590	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	76.1401	88	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.8102	87	977	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:15:22,983] [INFO] GTDB search result was written to OceanDNA-b24797/result_gtdb.tsv
[2023-03-14 11:15:22,983] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:15:22,984] [INFO] DFAST_QC result json was written to OceanDNA-b24797/dqc_result.json
[2023-03-14 11:15:22,984] [INFO] DFAST_QC completed!
[2023-03-14 11:15:22,984] [INFO] Total running time: 0h1m24s