[2023-03-18 23:27:53,699] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,699] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,699] [INFO] DQC Reference Directory: /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference
[2023-03-18 23:27:55,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,547] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stg5fea6bf3-c70a-4632-bbaf-f0bf7e3fbd0f/OceanDNA-b6500.fa | prodigal -d OceanDNA-b6500/cds.fna -a OceanDNA-b6500/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:08,722] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:08,722] [INFO] Task started: HMMsearch
[2023-03-18 23:28:08,722] [INFO] Running command: hmmsearch --tblout OceanDNA-b6500/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/reference_markers.hmm OceanDNA-b6500/protein.faa > /dev/null
[2023-03-18 23:28:08,910] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:08,911] [INFO] Found 6/6 markers.
[2023-03-18 23:28:08,926] [INFO] Query marker FASTA was written to OceanDNA-b6500/markers.fasta
[2023-03-18 23:28:08,927] [INFO] Task started: Blastn
[2023-03-18 23:28:08,927] [INFO] Running command: blastn -query OceanDNA-b6500/markers.fasta -db /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/reference_markers.fasta -out OceanDNA-b6500/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:09,470] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:09,471] [INFO] Selected 24 target genomes.
[2023-03-18 23:28:09,472] [INFO] Target genome list was writen to OceanDNA-b6500/target_genomes.txt
[2023-03-18 23:28:09,485] [INFO] Task started: fastANI
[2023-03-18 23:28:09,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fea6bf3-c70a-4632-bbaf-f0bf7e3fbd0f/OceanDNA-b6500.fa --refList OceanDNA-b6500/target_genomes.txt --output OceanDNA-b6500/fastani_result.tsv --threads 1
[2023-03-18 23:28:22,659] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:22,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:22,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:22,667] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:22,667] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:22,667] [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
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.3031	120	547	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.1927	111	547	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.1725	111	547	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.0151	93	547	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.7912	76	547	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	76.6461	61	547	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.4823	104	547	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.4185	77	547	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.1685	76	547	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:22,667] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6500/tc_result.tsv
[2023-03-18 23:28:22,667] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:22,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:22,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/checkm_data
[2023-03-18 23:28:22,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:22,689] [INFO] Task started: CheckM
[2023-03-18 23:28:22,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6500/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6500/checkm_input OceanDNA-b6500/checkm_result
[2023-03-18 23:28:58,984] [INFO] Task succeeded: CheckM
[2023-03-18 23:28:58,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:28:58,986] [INFO] ===== Completeness check finished =====
[2023-03-18 23:28:58,986] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:28:58,986] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6500/markers.fasta)
[2023-03-18 23:28:58,988] [INFO] Task started: Blastn
[2023-03-18 23:28:58,988] [INFO] Running command: blastn -query OceanDNA-b6500/markers.fasta -db /var/lib/cwl/stgee37af33-9c23-4f24-a670-e2c09b8d2511/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6500/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:59,692] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:59,693] [INFO] Selected 24 target genomes.
[2023-03-18 23:28:59,694] [INFO] Target genome list was writen to OceanDNA-b6500/target_genomes_gtdb.txt
[2023-03-18 23:28:59,715] [INFO] Task started: fastANI
[2023-03-18 23:28:59,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fea6bf3-c70a-4632-bbaf-f0bf7e3fbd0f/OceanDNA-b6500.fa --refList OceanDNA-b6500/target_genomes_gtdb.txt --output OceanDNA-b6500/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:11,800] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:11,809] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:29:11,809] [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_002813135.1	s__Altibacter sp002813135	78.213	198	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696485.1	s__Altibacter sp002696485	77.4145	114	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	99.86	99.86	0.91	0.91	2	-
GCF_000746845.1	s__Altibacter lentus	77.3031	120	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	77.1927	111	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014295415.1	s__Altibacter sp014295415	77.0151	93	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.7912	76	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.7505	79	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757735.1	s__Aequorivita sp016757735	76.6461	61	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043685.1	s__Pukyongia sp013043685	76.5802	53	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	-
GCF_003688405.1	s__Ulvibacter antarcticus	76.5184	102	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.4185	77	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002065.1	s__SMXJ01 sp013002065	76.2411	70	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	76.1854	75	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002715485.1	s__Aequorivita sp002715485	76.1814	60	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_002713705.1	s__GCA-002733185 sp002713705	75.7596	51	547	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:11,809] [INFO] GTDB search result was written to OceanDNA-b6500/result_gtdb.tsv
[2023-03-18 23:29:11,809] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:11,811] [INFO] DFAST_QC result json was written to OceanDNA-b6500/dqc_result.json
[2023-03-18 23:29:11,811] [INFO] DFAST_QC completed!
[2023-03-18 23:29:11,811] [INFO] Total running time: 0h1m18s