[2023-03-15 07:29:11,755] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference
[2023-03-15 07:29:13,589] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,589] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,589] [INFO] Running command: cat /var/lib/cwl/stgf399de4e-8f80-4f86-acb3-5acddcbee31f/OceanDNA-b24875.fa | prodigal -d OceanDNA-b24875/cds.fna -a OceanDNA-b24875/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:26,372] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:26,372] [INFO] Task started: HMMsearch
[2023-03-15 07:29:26,372] [INFO] Running command: hmmsearch --tblout OceanDNA-b24875/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/reference_markers.hmm OceanDNA-b24875/protein.faa > /dev/null
[2023-03-15 07:29:26,560] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:26,561] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf399de4e-8f80-4f86-acb3-5acddcbee31f/OceanDNA-b24875.fa]
[2023-03-15 07:29:26,579] [INFO] Query marker FASTA was written to OceanDNA-b24875/markers.fasta
[2023-03-15 07:29:26,579] [INFO] Task started: Blastn
[2023-03-15 07:29:26,579] [INFO] Running command: blastn -query OceanDNA-b24875/markers.fasta -db /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/reference_markers.fasta -out OceanDNA-b24875/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:27,270] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:27,271] [INFO] Selected 20 target genomes.
[2023-03-15 07:29:27,271] [INFO] Target genome list was writen to OceanDNA-b24875/target_genomes.txt
[2023-03-15 07:29:27,285] [INFO] Task started: fastANI
[2023-03-15 07:29:27,285] [INFO] Running command: fastANI --query /var/lib/cwl/stgf399de4e-8f80-4f86-acb3-5acddcbee31f/OceanDNA-b24875.fa --refList OceanDNA-b24875/target_genomes.txt --output OceanDNA-b24875/fastani_result.tsv --threads 1
[2023-03-15 07:29:40,277] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:40,277] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:40,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:40,284] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:40,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:40,284] [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
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	78.1492	268	634	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	77.677	215	634	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	77.3353	177	634	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	76.1835	52	634	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.1835	52	634	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.1014	94	634	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.0829	91	634	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	75.7289	56	634	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	75.7259	52	634	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:40,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24875/tc_result.tsv
[2023-03-15 07:29:40,284] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:40,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:40,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/checkm_data
[2023-03-15 07:29:40,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:40,289] [INFO] Task started: CheckM
[2023-03-15 07:29:40,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24875/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24875/checkm_input OceanDNA-b24875/checkm_result
[2023-03-15 07:30:15,998] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:15,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:16,001] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:16,001] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:16,001] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24875/markers.fasta)
[2023-03-15 07:30:16,003] [INFO] Task started: Blastn
[2023-03-15 07:30:16,003] [INFO] Running command: blastn -query OceanDNA-b24875/markers.fasta -db /var/lib/cwl/stg1a492535-dd27-46dd-8733-07ceb598c57f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24875/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:17,211] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:17,212] [INFO] Selected 12 target genomes.
[2023-03-15 07:30:17,212] [INFO] Target genome list was writen to OceanDNA-b24875/target_genomes_gtdb.txt
[2023-03-15 07:30:17,219] [INFO] Task started: fastANI
[2023-03-15 07:30:17,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgf399de4e-8f80-4f86-acb3-5acddcbee31f/OceanDNA-b24875.fa --refList OceanDNA-b24875/target_genomes_gtdb.txt --output OceanDNA-b24875/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:24,068] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:24,075] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:30:24,075] [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_009184905.1	s__Parvibaculum sedimenti	78.1492	268	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889655.1	s__Parvibaculum sp903889655	77.8065	276	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.81	99.81	0.91	0.91	2	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	77.6916	214	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	77.6727	202	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	77.4328	195	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_002842875.1	s__Parvibaculum sp002842875	77.415	188	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	77.3513	176	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684405.1	s__Parvibaculum sp002684405	77.3221	145	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124805.1	s__Parvibaculum sp016124805	77.295	191	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	77.1419	189	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_014359855.1	s__Parvibaculum sp014359855	77.1064	131	634	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:24,075] [INFO] GTDB search result was written to OceanDNA-b24875/result_gtdb.tsv
[2023-03-15 07:30:24,075] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:24,077] [INFO] DFAST_QC result json was written to OceanDNA-b24875/dqc_result.json
[2023-03-15 07:30:24,077] [INFO] DFAST_QC completed!
[2023-03-15 07:30:24,077] [INFO] Total running time: 0h1m12s