[2023-03-17 03:11:36,329] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:11:36,329] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:11:36,329] [INFO] DQC Reference Directory: /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference
[2023-03-17 03:11:37,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:11:37,522] [INFO] Task started: Prodigal
[2023-03-17 03:11:37,522] [INFO] Running command: cat /var/lib/cwl/stg90ef2885-9da7-40ce-a663-2457742363a4/OceanDNA-b6820.fa | prodigal -d OceanDNA-b6820/cds.fna -a OceanDNA-b6820/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:11:48,054] [INFO] Task succeeded: Prodigal
[2023-03-17 03:11:48,054] [INFO] Task started: HMMsearch
[2023-03-17 03:11:48,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b6820/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/reference_markers.hmm OceanDNA-b6820/protein.faa > /dev/null
[2023-03-17 03:11:48,264] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:11:48,265] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90ef2885-9da7-40ce-a663-2457742363a4/OceanDNA-b6820.fa]
[2023-03-17 03:11:48,294] [INFO] Query marker FASTA was written to OceanDNA-b6820/markers.fasta
[2023-03-17 03:11:48,295] [INFO] Task started: Blastn
[2023-03-17 03:11:48,295] [INFO] Running command: blastn -query OceanDNA-b6820/markers.fasta -db /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/reference_markers.fasta -out OceanDNA-b6820/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:11:48,858] [INFO] Task succeeded: Blastn
[2023-03-17 03:11:48,859] [INFO] Selected 17 target genomes.
[2023-03-17 03:11:48,859] [INFO] Target genome list was writen to OceanDNA-b6820/target_genomes.txt
[2023-03-17 03:11:48,935] [INFO] Task started: fastANI
[2023-03-17 03:11:48,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ef2885-9da7-40ce-a663-2457742363a4/OceanDNA-b6820.fa --refList OceanDNA-b6820/target_genomes.txt --output OceanDNA-b6820/fastani_result.tsv --threads 1
[2023-03-17 03:11:58,809] [INFO] Task succeeded: fastANI
[2023-03-17 03:11:58,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:11:58,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:11:58,819] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:11:58,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:11:58,819] [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	81.9855	303	453	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	78.0792	168	453	95	below_threshold
Flavobacterium jejuense	strain=EC11	GCA_006491595.2	1544455	1544455	type	True	77.8796	192	453	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	77.8121	165	453	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.7892	183	453	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.7731	183	453	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.766	170	453	95	below_threshold
Flavobacterium terrigena	strain=DSM 17934	GCA_900108955.1	402734	402734	type	True	77.5166	128	453	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	77.4703	148	453	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	77.4279	183	453	95	below_threshold
Flavobacterium urocaniciphilum	strain=DSM 27078	GCA_900110615.1	1299341	1299341	type	True	77.3752	128	453	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.3354	171	453	95	below_threshold
Flavobacterium bernardetii	strain=F-372	GCA_011305415.1	2813823	2813823	type	True	77.0103	136	453	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	76.9607	83	453	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	76.5701	110	453	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	76.2226	101	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:11:58,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6820/tc_result.tsv
[2023-03-17 03:11:58,820] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:11:58,820] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:11:58,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/checkm_data
[2023-03-17 03:11:58,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:11:58,834] [INFO] Task started: CheckM
[2023-03-17 03:11:58,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6820/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6820/checkm_input OceanDNA-b6820/checkm_result
[2023-03-17 03:12:30,065] [INFO] Task succeeded: CheckM
[2023-03-17 03:12:30,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:12:30,068] [INFO] ===== Completeness check finished =====
[2023-03-17 03:12:30,068] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:12:30,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6820/markers.fasta)
[2023-03-17 03:12:30,069] [INFO] Task started: Blastn
[2023-03-17 03:12:30,069] [INFO] Running command: blastn -query OceanDNA-b6820/markers.fasta -db /var/lib/cwl/stg94c4caed-fe0d-4f1e-8285-ff198c07f5c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6820/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:12:30,821] [INFO] Task succeeded: Blastn
[2023-03-17 03:12:30,822] [INFO] Selected 19 target genomes.
[2023-03-17 03:12:30,822] [INFO] Target genome list was writen to OceanDNA-b6820/target_genomes_gtdb.txt
[2023-03-17 03:12:31,008] [INFO] Task started: fastANI
[2023-03-17 03:12:31,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ef2885-9da7-40ce-a663-2457742363a4/OceanDNA-b6820.fa --refList OceanDNA-b6820/target_genomes_gtdb.txt --output OceanDNA-b6820/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:12:39,867] [INFO] Task succeeded: fastANI
[2023-03-17 03:12:39,878] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:12:39,878] [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_000422685.1	s__Flavobacterium gelidilacus	81.9855	303	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	78.0373	170	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862805.1	s__Flavobacterium sp002862805	78.0368	173	453	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	77.9001	179	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.75	96.74	0.84	0.84	3	-
GCA_003497625.1	s__Flavobacterium sp003497625	77.8837	170	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_006491595.2	s__Flavobacterium jejuense	77.8796	192	453	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	77.7131	180	453	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	77.706	154	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108955.1	s__Flavobacterium terrigena	77.5137	128	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006491645.1	s__Flavobacterium sp006491645	77.4279	183	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900110615.1	s__Flavobacterium urocaniciphilum	77.3981	127	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985075.1	s__Flavobacterium sp017985075	77.2498	111	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889745.1	s__Flavobacterium sp903889745	77.1759	114	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983975.1	s__Flavobacterium sp017983975	77.1275	114	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737105.1	s__Flavobacterium sp002737105	77.0207	50	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122165.1	s__Flavobacterium sp004122165	77.0147	82	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634825.1	s__Flavobacterium sp003634825	76.574	80	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	76.5701	110	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349315.1	s__Flavobacterium sp004349315	76.2074	102	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 03:12:39,878] [INFO] GTDB search result was written to OceanDNA-b6820/result_gtdb.tsv
[2023-03-17 03:12:39,878] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:12:39,880] [INFO] DFAST_QC result json was written to OceanDNA-b6820/dqc_result.json
[2023-03-17 03:12:39,880] [INFO] DFAST_QC completed!
[2023-03-17 03:12:39,880] [INFO] Total running time: 0h1m4s