[2023-03-18 23:27:53,696] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,696] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference
[2023-03-18 23:27:55,548] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,548] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stg4bd32d6f-0f18-4656-9a3c-7f8140da9759/OceanDNA-b6736.fa | prodigal -d OceanDNA-b6736/cds.fna -a OceanDNA-b6736/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:16,224] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:16,224] [INFO] Task started: HMMsearch
[2023-03-18 23:28:16,224] [INFO] Running command: hmmsearch --tblout OceanDNA-b6736/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/reference_markers.hmm OceanDNA-b6736/protein.faa > /dev/null
[2023-03-18 23:28:16,517] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:16,518] [INFO] Found 6/6 markers.
[2023-03-18 23:28:16,539] [INFO] Query marker FASTA was written to OceanDNA-b6736/markers.fasta
[2023-03-18 23:28:16,540] [INFO] Task started: Blastn
[2023-03-18 23:28:16,540] [INFO] Running command: blastn -query OceanDNA-b6736/markers.fasta -db /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/reference_markers.fasta -out OceanDNA-b6736/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:17,140] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:17,141] [INFO] Selected 25 target genomes.
[2023-03-18 23:28:17,141] [INFO] Target genome list was writen to OceanDNA-b6736/target_genomes.txt
[2023-03-18 23:28:17,156] [INFO] Task started: fastANI
[2023-03-18 23:28:17,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd32d6f-0f18-4656-9a3c-7f8140da9759/OceanDNA-b6736.fa --refList OceanDNA-b6736/target_genomes.txt --output OceanDNA-b6736/fastani_result.tsv --threads 1
[2023-03-18 23:28:33,045] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:33,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:33,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:33,058] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:33,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:33,058] [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
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	77.3251	191	987	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	77.2617	191	987	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	76.9846	136	987	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	76.9809	138	987	95	below_threshold
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	76.9629	196	987	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.3936	71	987	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3124	63	987	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.309	76	987	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.2554	68	987	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2328	65	987	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.2295	66	987	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	76.1942	70	987	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.1759	78	987	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	76.1647	63	987	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.1612	73	987	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.1002	64	987	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.0368	50	987	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.8519	57	987	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	75.8499	85	987	95	below_threshold
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	75.8285	56	987	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:33,058] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6736/tc_result.tsv
[2023-03-18 23:28:33,058] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:33,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:33,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/checkm_data
[2023-03-18 23:28:33,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:33,064] [INFO] Task started: CheckM
[2023-03-18 23:28:33,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6736/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6736/checkm_input OceanDNA-b6736/checkm_result
[2023-03-18 23:29:26,398] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:26,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:26,401] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:26,401] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:26,401] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6736/markers.fasta)
[2023-03-18 23:29:26,402] [INFO] Task started: Blastn
[2023-03-18 23:29:26,402] [INFO] Running command: blastn -query OceanDNA-b6736/markers.fasta -db /var/lib/cwl/stgbfaf99af-4063-4e27-af94-9b5d651e30d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6736/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:27,159] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:27,159] [INFO] Selected 23 target genomes.
[2023-03-18 23:29:27,160] [INFO] Target genome list was writen to OceanDNA-b6736/target_genomes_gtdb.txt
[2023-03-18 23:29:27,179] [INFO] Task started: fastANI
[2023-03-18 23:29:27,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd32d6f-0f18-4656-9a3c-7f8140da9759/OceanDNA-b6736.fa --refList OceanDNA-b6736/target_genomes_gtdb.txt --output OceanDNA-b6736/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:40,367] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:40,379] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:29:40,379] [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_002712765.1	s__Dokdonia sp002712765	78.1825	206	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	99.61	99.61	0.82	0.82	2	-
GCF_003095655.1	s__Dokdonia sp003095655	77.2975	143	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188275.1	s__Dokdonia pacifica	77.2617	191	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000355805.1	s__Dokdonia sp000355805	77.0205	146	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212355.1	s__Dokdonia sp000212355	77.0122	146	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_001653755.1	s__Dokdonia donghaensis	76.9809	138	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCF_003688895.1	s__Dokdonia sinensis	76.9629	196	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	76.4906	59	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099995.1	s__Winogradskyella thalassocola	76.3936	71	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	76.3568	74	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_016785945.1	s__Olleya sediminilitoris	76.3552	56	987	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	76.3128	82	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	76.237	67	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_002831645.1	s__Olleya sp002831645	76.2316	72	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003144015.1	s__Xanthomarina sp003144015	76.1856	74	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900112395.1	s__Algibacter lectus	76.1529	72	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_013403985.1	s__Winogradskyella ludwigii	76.1002	64	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796825.1	s__Algibacter sp009796825	76.041	65	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	76.0196	67	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_009796805.1	s__Algibacter sp009796805	75.9903	78	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934685.1	s__Lacinutrix sp000934685	75.9709	63	987	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:40,379] [INFO] GTDB search result was written to OceanDNA-b6736/result_gtdb.tsv
[2023-03-18 23:29:40,379] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:40,382] [INFO] DFAST_QC result json was written to OceanDNA-b6736/dqc_result.json
[2023-03-18 23:29:40,382] [INFO] DFAST_QC completed!
[2023-03-18 23:29:40,382] [INFO] Total running time: 0h1m47s