[2023-03-16 05:17:36,703] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:17:36,704] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:17:36,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference
[2023-03-16 05:17:37,893] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:17:37,893] [INFO] Task started: Prodigal
[2023-03-16 05:17:37,893] [INFO] Running command: cat /var/lib/cwl/stgd261d390-3800-4269-899e-e07c86d23394/OceanDNA-b24965.fa | prodigal -d OceanDNA-b24965/cds.fna -a OceanDNA-b24965/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:17:58,819] [INFO] Task succeeded: Prodigal
[2023-03-16 05:17:58,820] [INFO] Task started: HMMsearch
[2023-03-16 05:17:58,820] [INFO] Running command: hmmsearch --tblout OceanDNA-b24965/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/reference_markers.hmm OceanDNA-b24965/protein.faa > /dev/null
[2023-03-16 05:17:59,020] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:17:59,021] [INFO] Found 6/6 markers.
[2023-03-16 05:17:59,072] [INFO] Query marker FASTA was written to OceanDNA-b24965/markers.fasta
[2023-03-16 05:17:59,072] [INFO] Task started: Blastn
[2023-03-16 05:17:59,073] [INFO] Running command: blastn -query OceanDNA-b24965/markers.fasta -db /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/reference_markers.fasta -out OceanDNA-b24965/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:17:59,798] [INFO] Task succeeded: Blastn
[2023-03-16 05:17:59,804] [INFO] Selected 22 target genomes.
[2023-03-16 05:17:59,804] [INFO] Target genome list was writen to OceanDNA-b24965/target_genomes.txt
[2023-03-16 05:17:59,829] [INFO] Task started: fastANI
[2023-03-16 05:17:59,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgd261d390-3800-4269-899e-e07c86d23394/OceanDNA-b24965.fa --refList OceanDNA-b24965/target_genomes.txt --output OceanDNA-b24965/fastani_result.tsv --threads 1
[2023-03-16 05:18:16,139] [INFO] Task succeeded: fastANI
[2023-03-16 05:18:16,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:18:16,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:18:16,147] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:18:16,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:18:16,147] [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
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	79.2196	537	1071	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	79.1519	551	1071	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	79.1143	540	1071	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.36	51	1071	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.2395	129	1071	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.1678	98	1071	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.0092	54	1071	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.9371	62	1071	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	75.8166	96	1071	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	75.8008	51	1071	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	75.4012	53	1071	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:18:16,150] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24965/tc_result.tsv
[2023-03-16 05:18:16,150] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:18:16,150] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:18:16,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/checkm_data
[2023-03-16 05:18:16,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:18:16,157] [INFO] Task started: CheckM
[2023-03-16 05:18:16,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24965/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24965/checkm_input OceanDNA-b24965/checkm_result
[2023-03-16 05:19:09,427] [INFO] Task succeeded: CheckM
[2023-03-16 05:19:09,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:19:09,527] [INFO] ===== Completeness check finished =====
[2023-03-16 05:19:09,528] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:19:09,528] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24965/markers.fasta)
[2023-03-16 05:19:09,529] [INFO] Task started: Blastn
[2023-03-16 05:19:09,529] [INFO] Running command: blastn -query OceanDNA-b24965/markers.fasta -db /var/lib/cwl/stg9f6c21e0-396b-4de2-be96-8ff17c17ce15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24965/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:19:10,861] [INFO] Task succeeded: Blastn
[2023-03-16 05:19:10,868] [INFO] Selected 24 target genomes.
[2023-03-16 05:19:10,868] [INFO] Target genome list was writen to OceanDNA-b24965/target_genomes_gtdb.txt
[2023-03-16 05:19:10,888] [INFO] Task started: fastANI
[2023-03-16 05:19:10,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgd261d390-3800-4269-899e-e07c86d23394/OceanDNA-b24965.fa --refList OceanDNA-b24965/target_genomes_gtdb.txt --output OceanDNA-b24965/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:19:25,814] [INFO] Task succeeded: fastANI
[2023-03-16 05:19:25,825] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:19:25,826] [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_000689395.1	s__Pyruvatibacter ectocarpi	88.8715	956	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848855.1	s__Pyruvatibacter mobilis	79.2193	538	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002684405.1	s__Parvibaculum sp002684405	76.5893	96	1071	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	76.3848	99	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_002480495.1	s__Parvibaculum sp002480495	76.3753	98	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	76.36	51	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	76.3436	86	1071	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	76.2395	129	1071	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	76.2362	106	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	76.1678	98	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629525.1	s__Kaistia sp016629525	76.0936	52	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	75.9334	90	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	75.8456	55	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184905.1	s__Parvibaculum sedimenti	75.8166	96	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124385.1	s__JACADY01 sp016124385	75.7509	57	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__JACADY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.7095	57	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018334155.1	s__Devosia sp018334155	75.6696	50	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473085.1	s__Azorhizobium doebereinerae	75.5527	84	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	75.4012	53	1071	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:19:25,829] [INFO] GTDB search result was written to OceanDNA-b24965/result_gtdb.tsv
[2023-03-16 05:19:25,831] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:19:25,835] [INFO] DFAST_QC result json was written to OceanDNA-b24965/dqc_result.json
[2023-03-16 05:19:25,835] [INFO] DFAST_QC completed!
[2023-03-16 05:19:25,835] [INFO] Total running time: 0h1m49s