[2023-03-16 18:09:00,104] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:09:00,104] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:09:00,104] [INFO] DQC Reference Directory: /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference
[2023-03-16 18:09:01,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:09:01,197] [INFO] Task started: Prodigal
[2023-03-16 18:09:01,197] [INFO] Running command: cat /var/lib/cwl/stgb7963025-1ebf-4930-9120-bd164ce44a6f/OceanDNA-b6817.fa | prodigal -d OceanDNA-b6817/cds.fna -a OceanDNA-b6817/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:09:07,092] [INFO] Task succeeded: Prodigal
[2023-03-16 18:09:07,092] [INFO] Task started: HMMsearch
[2023-03-16 18:09:07,092] [INFO] Running command: hmmsearch --tblout OceanDNA-b6817/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/reference_markers.hmm OceanDNA-b6817/protein.faa > /dev/null
[2023-03-16 18:09:07,246] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:09:07,247] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb7963025-1ebf-4930-9120-bd164ce44a6f/OceanDNA-b6817.fa]
[2023-03-16 18:09:07,259] [INFO] Query marker FASTA was written to OceanDNA-b6817/markers.fasta
[2023-03-16 18:09:07,260] [INFO] Task started: Blastn
[2023-03-16 18:09:07,260] [INFO] Running command: blastn -query OceanDNA-b6817/markers.fasta -db /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/reference_markers.fasta -out OceanDNA-b6817/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:07,909] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:07,909] [INFO] Selected 15 target genomes.
[2023-03-16 18:09:07,910] [INFO] Target genome list was writen to OceanDNA-b6817/target_genomes.txt
[2023-03-16 18:09:07,915] [INFO] Task started: fastANI
[2023-03-16 18:09:07,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7963025-1ebf-4930-9120-bd164ce44a6f/OceanDNA-b6817.fa --refList OceanDNA-b6817/target_genomes.txt --output OceanDNA-b6817/fastani_result.tsv --threads 1
[2023-03-16 18:09:14,956] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:14,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:09:14,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:09:14,966] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:09:14,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:09:14,966] [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
Flavobacterium gelidilacus	strain=DSM 15343	GCA_000422685.1	206041	206041	type	True	80.2133	134	210	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	78.6365	131	210	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.2615	135	210	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	78.1544	116	210	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	78.1168	107	210	95	below_threshold
Flavobacterium tibetense	strain=YH5	GCA_003293845.1	2233533	2233533	type	True	78.1034	93	210	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_006491645.1	1774945	1774945	type	True	78.0802	108	210	95	below_threshold
Flavobacterium cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	77.9717	121	210	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	77.9571	106	210	95	below_threshold
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	77.9441	122	210	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.9427	111	210	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.8711	111	210	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	77.6317	87	210	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	76.7818	50	210	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	76.6496	63	210	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:09:14,966] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6817/tc_result.tsv
[2023-03-16 18:09:14,966] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:09:14,966] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:09:14,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/checkm_data
[2023-03-16 18:09:14,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:09:14,974] [INFO] Task started: CheckM
[2023-03-16 18:09:14,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6817/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6817/checkm_input OceanDNA-b6817/checkm_result
[2023-03-16 18:09:35,397] [INFO] Task succeeded: CheckM
[2023-03-16 18:09:35,398] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:09:35,399] [INFO] ===== Completeness check finished =====
[2023-03-16 18:09:35,400] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:09:35,400] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6817/markers.fasta)
[2023-03-16 18:09:35,401] [INFO] Task started: Blastn
[2023-03-16 18:09:35,401] [INFO] Running command: blastn -query OceanDNA-b6817/markers.fasta -db /var/lib/cwl/stg81efb4e9-c03e-46ce-916d-1802a8dcdf26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6817/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:09:36,250] [INFO] Task succeeded: Blastn
[2023-03-16 18:09:36,251] [INFO] Selected 13 target genomes.
[2023-03-16 18:09:36,251] [INFO] Target genome list was writen to OceanDNA-b6817/target_genomes_gtdb.txt
[2023-03-16 18:09:36,280] [INFO] Task started: fastANI
[2023-03-16 18:09:36,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7963025-1ebf-4930-9120-bd164ce44a6f/OceanDNA-b6817.fa --refList OceanDNA-b6817/target_genomes_gtdb.txt --output OceanDNA-b6817/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:09:42,680] [INFO] Task succeeded: fastANI
[2023-03-16 18:09:42,687] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:09:42,687] [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_002862805.1	s__Flavobacterium sp002862805	81.847	185	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422685.1	s__Flavobacterium gelidilacus	80.2133	134	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491595.2	s__Flavobacterium jejuense	78.6487	130	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497625.1	s__Flavobacterium sp003497625	78.4901	102	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009495755.1	s__Flavobacterium sp009495755	78.2715	118	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	78.2674	137	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000169355.1	s__Flavobacterium sp000169355	78.2178	112	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCF_006491645.1	s__Flavobacterium sp006491645	78.1168	107	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003293845.1	s__Flavobacterium tibetense	78.0571	95	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032075.1	s__Flavobacterium sp012032075	78.0386	113	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506265.1	s__Flavobacterium sp902506265	77.9711	118	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401995.1	s__Flavobacterium sp018401995	77.7638	77	210	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:09:42,690] [INFO] GTDB search result was written to OceanDNA-b6817/result_gtdb.tsv
[2023-03-16 18:09:42,690] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:09:42,692] [INFO] DFAST_QC result json was written to OceanDNA-b6817/dqc_result.json
[2023-03-16 18:09:42,692] [INFO] DFAST_QC completed!
[2023-03-16 18:09:42,692] [INFO] Total running time: 0h0m43s