[2023-03-18 08:31:56,271] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,271] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,271] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference
[2023-03-18 08:31:57,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,415] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,415] [INFO] Running command: cat /var/lib/cwl/stg3e1a7c8c-d23f-422f-b7ce-98fb95964450/OceanDNA-b6425.fa | prodigal -d OceanDNA-b6425/cds.fna -a OceanDNA-b6425/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:21,961] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:21,962] [INFO] Task started: HMMsearch
[2023-03-18 08:32:21,962] [INFO] Running command: hmmsearch --tblout OceanDNA-b6425/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/reference_markers.hmm OceanDNA-b6425/protein.faa > /dev/null
[2023-03-18 08:32:22,155] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:22,155] [INFO] Found 6/6 markers.
[2023-03-18 08:32:22,175] [INFO] Query marker FASTA was written to OceanDNA-b6425/markers.fasta
[2023-03-18 08:32:22,175] [INFO] Task started: Blastn
[2023-03-18 08:32:22,176] [INFO] Running command: blastn -query OceanDNA-b6425/markers.fasta -db /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/reference_markers.fasta -out OceanDNA-b6425/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:22,760] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:22,760] [INFO] Selected 11 target genomes.
[2023-03-18 08:32:22,761] [INFO] Target genome list was writen to OceanDNA-b6425/target_genomes.txt
[2023-03-18 08:32:22,766] [INFO] Task started: fastANI
[2023-03-18 08:32:22,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1a7c8c-d23f-422f-b7ce-98fb95964450/OceanDNA-b6425.fa --refList OceanDNA-b6425/target_genomes.txt --output OceanDNA-b6425/fastani_result.tsv --threads 1
[2023-03-18 08:32:30,417] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:30,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:30,418] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:30,424] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:30,425] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:30,425] [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 iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	83.0503	784	1100	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	81.5837	679	1100	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	81.2551	652	1100	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	81.0746	656	1100	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.6372	623	1100	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	80.2966	619	1100	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.5105	522	1100	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	78.6882	443	1100	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.7503	50	1100	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.7083	52	1100	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:30,425] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6425/tc_result.tsv
[2023-03-18 08:32:30,425] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:30,425] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:30,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/checkm_data
[2023-03-18 08:32:30,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:30,447] [INFO] Task started: CheckM
[2023-03-18 08:32:30,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6425/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6425/checkm_input OceanDNA-b6425/checkm_result
[2023-03-18 08:33:31,486] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:31,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:33:31,489] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:31,489] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:31,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6425/markers.fasta)
[2023-03-18 08:33:31,490] [INFO] Task started: Blastn
[2023-03-18 08:33:31,490] [INFO] Running command: blastn -query OceanDNA-b6425/markers.fasta -db /var/lib/cwl/stgfda54b6a-956b-4634-8c11-610354380d91/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6425/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:32,272] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:32,273] [INFO] Selected 11 target genomes.
[2023-03-18 08:33:32,273] [INFO] Target genome list was writen to OceanDNA-b6425/target_genomes_gtdb.txt
[2023-03-18 08:33:32,302] [INFO] Task started: fastANI
[2023-03-18 08:33:32,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e1a7c8c-d23f-422f-b7ce-98fb95964450/OceanDNA-b6425.fa --refList OceanDNA-b6425/target_genomes_gtdb.txt --output OceanDNA-b6425/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:33:40,201] [INFO] Task succeeded: fastANI
[2023-03-18 08:33:40,208] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:33:40,208] [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_002733915.1	s__Aequorivita sp002733915	83.5293	762	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	83.0337	786	1100	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	82.0585	636	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_002364215.1	s__Aequorivita sp002364215	81.7352	715	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001573155.1	s__Aequorivita aquimaris	81.5837	679	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	81.2448	653	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_001641085.1	s__Aequorivita soesokkakensis	81.0746	656	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_900489465.1	s__Aequorivita sp900489465	80.3516	628	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997155.1	s__Aequorivita antarctica	80.2878	620	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCA_016649715.1	s__Aequorivita sp016649715	80.1852	553	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265385.1	s__Aequorivita sublithincola	79.5054	522	1100	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:33:40,209] [INFO] GTDB search result was written to OceanDNA-b6425/result_gtdb.tsv
[2023-03-18 08:33:40,209] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:33:40,210] [INFO] DFAST_QC result json was written to OceanDNA-b6425/dqc_result.json
[2023-03-18 08:33:40,210] [INFO] DFAST_QC completed!
[2023-03-18 08:33:40,210] [INFO] Total running time: 0h1m44s