[2023-03-19 00:48:24,537] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:48:24,537] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:48:24,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference
[2023-03-19 00:48:26,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:48:26,001] [INFO] Task started: Prodigal
[2023-03-19 00:48:26,001] [INFO] Running command: cat /var/lib/cwl/stg19b455ea-a57d-43ad-934c-00460baedca4/OceanDNA-b9724.fa | prodigal -d OceanDNA-b9724/cds.fna -a OceanDNA-b9724/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:48:35,526] [INFO] Task succeeded: Prodigal
[2023-03-19 00:48:35,527] [INFO] Task started: HMMsearch
[2023-03-19 00:48:35,527] [INFO] Running command: hmmsearch --tblout OceanDNA-b9724/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/reference_markers.hmm OceanDNA-b9724/protein.faa > /dev/null
[2023-03-19 00:48:35,701] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:48:35,702] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg19b455ea-a57d-43ad-934c-00460baedca4/OceanDNA-b9724.fa]
[2023-03-19 00:48:35,719] [INFO] Query marker FASTA was written to OceanDNA-b9724/markers.fasta
[2023-03-19 00:48:35,720] [INFO] Task started: Blastn
[2023-03-19 00:48:35,721] [INFO] Running command: blastn -query OceanDNA-b9724/markers.fasta -db /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/reference_markers.fasta -out OceanDNA-b9724/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:48:36,259] [INFO] Task succeeded: Blastn
[2023-03-19 00:48:36,260] [INFO] Selected 22 target genomes.
[2023-03-19 00:48:36,260] [INFO] Target genome list was writen to OceanDNA-b9724/target_genomes.txt
[2023-03-19 00:48:36,277] [INFO] Task started: fastANI
[2023-03-19 00:48:36,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b455ea-a57d-43ad-934c-00460baedca4/OceanDNA-b9724.fa --refList OceanDNA-b9724/target_genomes.txt --output OceanDNA-b9724/fastani_result.tsv --threads 1
[2023-03-19 00:48:48,370] [INFO] Task succeeded: fastANI
[2023-03-19 00:48:48,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:48:48,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:48:48,383] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 00:48:48,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 00:48:48,383] [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
Aurantibacter aestuarii	strain=KCTC 32269	GCA_003008425.1	1266046	1266046	type	True	96.7497	408	444	95	conclusive
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	77.979	131	444	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.9281	133	444	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.8078	95	444	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.6948	103	444	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	77.6884	115	444	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.6866	138	444	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.6756	91	444	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.6717	134	444	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.5756	107	444	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5747	132	444	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.5656	108	444	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.5656	108	444	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	77.5202	154	444	95	below_threshold
Winogradskyella epiphytica	strain=KCTC 12220	GCA_014651315.1	262005	262005	type	True	77.5147	75	444	95	below_threshold
Winogradskyella epiphytica	strain=CECT 7945	GCA_003217215.1	262005	262005	type	True	77.4284	75	444	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.3678	78	444	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.307	105	444	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.9218	101	444	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9211	56	444	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.8689	71	444	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:48:48,384] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9724/tc_result.tsv
[2023-03-19 00:48:48,384] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:48:48,384] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:48:48,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/checkm_data
[2023-03-19 00:48:48,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:48:48,389] [INFO] Task started: CheckM
[2023-03-19 00:48:48,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9724/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9724/checkm_input OceanDNA-b9724/checkm_result
[2023-03-19 00:49:17,013] [INFO] Task succeeded: CheckM
[2023-03-19 00:49:17,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:49:17,092] [INFO] ===== Completeness check finished =====
[2023-03-19 00:49:17,092] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:49:17,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9724/markers.fasta)
[2023-03-19 00:49:17,096] [INFO] Task started: Blastn
[2023-03-19 00:49:17,096] [INFO] Running command: blastn -query OceanDNA-b9724/markers.fasta -db /var/lib/cwl/stgc952af98-82d0-4a37-b6d6-2cef26ac3095/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9724/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:49:17,854] [INFO] Task succeeded: Blastn
[2023-03-19 00:49:17,856] [INFO] Selected 21 target genomes.
[2023-03-19 00:49:17,856] [INFO] Target genome list was writen to OceanDNA-b9724/target_genomes_gtdb.txt
[2023-03-19 00:49:17,871] [INFO] Task started: fastANI
[2023-03-19 00:49:17,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg19b455ea-a57d-43ad-934c-00460baedca4/OceanDNA-b9724.fa --refList OceanDNA-b9724/target_genomes_gtdb.txt --output OceanDNA-b9724/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:49:29,876] [INFO] Task succeeded: fastANI
[2023-03-19 00:49:29,888] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:49:29,888] [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_003008425.1	s__Aurantibacter aestuarii	96.7497	408	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003663945.1	s__Lacinutrix venerupis	77.9996	145	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	77.9515	132	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_003259525.1	s__Olleya aquimaris	77.9281	133	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831665.1	s__Lacinutrix sp002831665	77.8715	139	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874145.1	s__Lacinutrix sp001874145	77.862	150	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	77.7714	153	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_001418085.1	s__Lacinutrix algicola	77.7601	149	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.7342	136	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	77.7196	93	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.6948	103	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	77.6925	99	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	77.6884	115	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518485.1	s__Olleya marilimosa	77.6717	134	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_000211855.2	s__Lacinutrix sp000211855	77.6519	160	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	77.6367	140	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.5756	107	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.5747	132	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	77.5202	154	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
GCF_003217215.1	s__Winogradskyella epiphytica	77.4284	75	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014297365.1	s__Winogradskyella echinorum	77.4187	93	444	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:49:29,889] [INFO] GTDB search result was written to OceanDNA-b9724/result_gtdb.tsv
[2023-03-19 00:49:29,890] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:49:29,893] [INFO] DFAST_QC result json was written to OceanDNA-b9724/dqc_result.json
[2023-03-19 00:49:29,894] [INFO] DFAST_QC completed!
[2023-03-19 00:49:29,894] [INFO] Total running time: 0h1m5s