[2023-03-16 10:13:35,973] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:13:35,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:13:35,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference
[2023-03-16 10:13:37,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:13:37,157] [INFO] Task started: Prodigal
[2023-03-16 10:13:37,157] [INFO] Running command: cat /var/lib/cwl/stg0cf0dc60-d1b9-4eb1-b2cd-7dc489bf0d7b/OceanDNA-b10085.fa | prodigal -d OceanDNA-b10085/cds.fna -a OceanDNA-b10085/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:14:08,301] [INFO] Task succeeded: Prodigal
[2023-03-16 10:14:08,301] [INFO] Task started: HMMsearch
[2023-03-16 10:14:08,301] [INFO] Running command: hmmsearch --tblout OceanDNA-b10085/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/reference_markers.hmm OceanDNA-b10085/protein.faa > /dev/null
[2023-03-16 10:14:08,525] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:14:08,525] [INFO] Found 6/6 markers.
[2023-03-16 10:14:08,553] [INFO] Query marker FASTA was written to OceanDNA-b10085/markers.fasta
[2023-03-16 10:14:08,554] [INFO] Task started: Blastn
[2023-03-16 10:14:08,554] [INFO] Running command: blastn -query OceanDNA-b10085/markers.fasta -db /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/reference_markers.fasta -out OceanDNA-b10085/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:14:11,557] [INFO] Task succeeded: Blastn
[2023-03-16 10:14:11,559] [INFO] Selected 24 target genomes.
[2023-03-16 10:14:11,559] [INFO] Target genome list was writen to OceanDNA-b10085/target_genomes.txt
[2023-03-16 10:14:11,616] [INFO] Task started: fastANI
[2023-03-16 10:14:11,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cf0dc60-d1b9-4eb1-b2cd-7dc489bf0d7b/OceanDNA-b10085.fa --refList OceanDNA-b10085/target_genomes.txt --output OceanDNA-b10085/fastani_result.tsv --threads 1
[2023-03-16 10:14:28,179] [INFO] Task succeeded: fastANI
[2023-03-16 10:14:28,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:14:28,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:14:28,190] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 10:14:28,190] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 10:14:28,190] [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
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	97.2171	1321	1443	95	conclusive
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	79.4957	515	1443	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	77.1155	232	1443	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	77.0561	234	1443	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.0173	222	1443	95	below_threshold
Pareuzebyella sediminis	strain=S2-4-21	GCA_008367235.1	2607998	2607998	type	True	77.0124	176	1443	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	76.8467	233	1443	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.6055	123	1443	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.3507	145	1443	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	76.2907	111	1443	95	below_threshold
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	76.0047	96	1443	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.0016	93	1443	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	75.8987	86	1443	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	75.7934	119	1443	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.6789	81	1443	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	75.611	83	1443	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	75.4569	52	1443	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:14:28,191] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10085/tc_result.tsv
[2023-03-16 10:14:28,191] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:14:28,191] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:14:28,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/checkm_data
[2023-03-16 10:14:28,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:14:28,341] [INFO] Task started: CheckM
[2023-03-16 10:14:28,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10085/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10085/checkm_input OceanDNA-b10085/checkm_result
[2023-03-16 10:15:44,516] [INFO] Task succeeded: CheckM
[2023-03-16 10:15:44,516] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:15:44,522] [INFO] ===== Completeness check finished =====
[2023-03-16 10:15:44,522] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:15:44,522] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10085/markers.fasta)
[2023-03-16 10:15:44,524] [INFO] Task started: Blastn
[2023-03-16 10:15:44,524] [INFO] Running command: blastn -query OceanDNA-b10085/markers.fasta -db /var/lib/cwl/stg0bab601c-0202-4386-82c8-0c2bea703075/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10085/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:15:45,313] [INFO] Task succeeded: Blastn
[2023-03-16 10:15:45,316] [INFO] Selected 26 target genomes.
[2023-03-16 10:15:45,316] [INFO] Target genome list was writen to OceanDNA-b10085/target_genomes_gtdb.txt
[2023-03-16 10:15:45,434] [INFO] Task started: fastANI
[2023-03-16 10:15:45,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cf0dc60-d1b9-4eb1-b2cd-7dc489bf0d7b/OceanDNA-b10085.fa --refList OceanDNA-b10085/target_genomes_gtdb.txt --output OceanDNA-b10085/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:16:03,014] [INFO] Task succeeded: fastANI
[2023-03-16 10:16:03,024] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:16:03,025] [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_014855515.1	s__Euzebyella marina	97.2171	1321	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	conclusive
GCF_014349235.1	s__Euzebyella sp014349235	81.3286	532	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855495.1	s__Euzebyella saccharophila	79.5006	514	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017810075.1	s__Pseudozobellia sp017810075	78.4048	431	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813285.1	s__Pseudozobellia sp002813285	77.9635	432	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	77.5116	310	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	77.1155	232	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	77.0561	234	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_018728565.1	s__Zobellia russellii	76.8569	232	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_018860745.1	s__Zobellia uliginosa_B	76.7228	209	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232155.1	s__RZ26 sp003232155	76.5729	75	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__RZ26	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933245.1	s__Maribacter algicola	76.2907	111	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050085.1	s__Pricia antarctica_A	76.2429	130	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232435.1	s__Aurantibacter_A sp003232435	76.0199	83	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	76.0016	93	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001935.1	s__Maribacter_A sp013001935	75.8816	61	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	96.76	96.72	0.66	0.66	3	-
GCF_000733925.1	s__Arenibacter algicola	75.7934	119	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_007785775.2	s__Muricauda sp003973595	75.6938	80	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_009184425.1	s__Muricauda olearia	75.6256	82	1443	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:16:03,026] [INFO] GTDB search result was written to OceanDNA-b10085/result_gtdb.tsv
[2023-03-16 10:16:03,026] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:16:03,029] [INFO] DFAST_QC result json was written to OceanDNA-b10085/dqc_result.json
[2023-03-16 10:16:03,029] [INFO] DFAST_QC completed!
[2023-03-16 10:16:03,029] [INFO] Total running time: 0h2m27s