[2023-03-14 11:17:29,599] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:17:29,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:17:29,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference
[2023-03-14 11:17:30,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:17:30,691] [INFO] Task started: Prodigal
[2023-03-14 11:17:30,691] [INFO] Running command: cat /var/lib/cwl/stga07b4b55-f617-46b9-9395-86640020aaf1/OceanDNA-b6457.fa | prodigal -d OceanDNA-b6457/cds.fna -a OceanDNA-b6457/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:17:53,007] [INFO] Task succeeded: Prodigal
[2023-03-14 11:17:53,008] [INFO] Task started: HMMsearch
[2023-03-14 11:17:53,008] [INFO] Running command: hmmsearch --tblout OceanDNA-b6457/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/reference_markers.hmm OceanDNA-b6457/protein.faa > /dev/null
[2023-03-14 11:17:53,211] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:17:53,211] [INFO] Found 6/6 markers.
[2023-03-14 11:17:53,229] [INFO] Query marker FASTA was written to OceanDNA-b6457/markers.fasta
[2023-03-14 11:17:53,231] [INFO] Task started: Blastn
[2023-03-14 11:17:53,231] [INFO] Running command: blastn -query OceanDNA-b6457/markers.fasta -db /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/reference_markers.fasta -out OceanDNA-b6457/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:17:53,832] [INFO] Task succeeded: Blastn
[2023-03-14 11:17:53,833] [INFO] Selected 11 target genomes.
[2023-03-14 11:17:53,833] [INFO] Target genome list was writen to OceanDNA-b6457/target_genomes.txt
[2023-03-14 11:17:53,840] [INFO] Task started: fastANI
[2023-03-14 11:17:53,840] [INFO] Running command: fastANI --query /var/lib/cwl/stga07b4b55-f617-46b9-9395-86640020aaf1/OceanDNA-b6457.fa --refList OceanDNA-b6457/target_genomes.txt --output OceanDNA-b6457/fastani_result.tsv --threads 1
[2023-03-14 11:18:01,179] [INFO] Task succeeded: fastANI
[2023-03-14 11:18:01,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:18:01,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:18:01,186] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 11:18:01,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 11:18:01,187] [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
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	98.3026	916	967	95	conclusive
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	91.2213	796	967	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	82.8124	700	967	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	82.0101	640	967	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.2117	589	967	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	79.889	601	967	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	78.894	545	967	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:18:01,187] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6457/tc_result.tsv
[2023-03-14 11:18:01,187] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:18:01,187] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:18:01,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/checkm_data
[2023-03-14 11:18:01,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:18:01,743] [INFO] Task started: CheckM
[2023-03-14 11:18:01,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6457/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6457/checkm_input OceanDNA-b6457/checkm_result
[2023-03-14 11:18:58,765] [INFO] Task succeeded: CheckM
[2023-03-14 11:18:58,765] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:18:58,767] [INFO] ===== Completeness check finished =====
[2023-03-14 11:18:58,768] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:18:58,768] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6457/markers.fasta)
[2023-03-14 11:18:58,769] [INFO] Task started: Blastn
[2023-03-14 11:18:58,769] [INFO] Running command: blastn -query OceanDNA-b6457/markers.fasta -db /var/lib/cwl/stg68c7fedc-3a60-4892-819f-9a00b09dbc7a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6457/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:18:59,535] [INFO] Task succeeded: Blastn
[2023-03-14 11:18:59,536] [INFO] Selected 8 target genomes.
[2023-03-14 11:18:59,536] [INFO] Target genome list was writen to OceanDNA-b6457/target_genomes_gtdb.txt
[2023-03-14 11:18:59,546] [INFO] Task started: fastANI
[2023-03-14 11:18:59,546] [INFO] Running command: fastANI --query /var/lib/cwl/stga07b4b55-f617-46b9-9395-86640020aaf1/OceanDNA-b6457.fa --refList OceanDNA-b6457/target_genomes_gtdb.txt --output OceanDNA-b6457/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:19:05,073] [INFO] Task succeeded: fastANI
[2023-03-14 11:19:05,079] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:19:05,079] [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_000952855.1	s__Aequorivita vladivostokensis	98.3026	916	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	conclusive
GCF_001573155.1	s__Aequorivita aquimaris	91.2213	796	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	84.9162	763	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_016757735.1	s__Aequorivita sp016757735	82.8124	700	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	82.0746	634	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_001641085.1	s__Aequorivita soesokkakensis	82.0101	640	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCA_002733915.1	s__Aequorivita sp002733915	81.8705	675	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649715.1	s__Aequorivita sp016649715	80.2037	560	967	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:19:05,080] [INFO] GTDB search result was written to OceanDNA-b6457/result_gtdb.tsv
[2023-03-14 11:19:05,080] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:19:05,081] [INFO] DFAST_QC result json was written to OceanDNA-b6457/dqc_result.json
[2023-03-14 11:19:05,081] [INFO] DFAST_QC completed!
[2023-03-14 11:19:05,081] [INFO] Total running time: 0h1m35s