[2023-03-18 20:55:47,242] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,243] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stg8a85b454-27aa-47da-98c8-1360ea8d80a2/OceanDNA-b6783.fa | prodigal -d OceanDNA-b6783/cds.fna -a OceanDNA-b6783/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:56:06,405] [INFO] Task succeeded: Prodigal
[2023-03-18 20:56:06,406] [INFO] Task started: HMMsearch
[2023-03-18 20:56:06,406] [INFO] Running command: hmmsearch --tblout OceanDNA-b6783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/reference_markers.hmm OceanDNA-b6783/protein.faa > /dev/null
[2023-03-18 20:56:06,587] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:56:06,587] [INFO] Found 6/6 markers.
[2023-03-18 20:56:06,603] [INFO] Query marker FASTA was written to OceanDNA-b6783/markers.fasta
[2023-03-18 20:56:06,604] [INFO] Task started: Blastn
[2023-03-18 20:56:06,604] [INFO] Running command: blastn -query OceanDNA-b6783/markers.fasta -db /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/reference_markers.fasta -out OceanDNA-b6783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:07,231] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:07,231] [INFO] Selected 26 target genomes.
[2023-03-18 20:56:07,232] [INFO] Target genome list was writen to OceanDNA-b6783/target_genomes.txt
[2023-03-18 20:56:07,246] [INFO] Task started: fastANI
[2023-03-18 20:56:07,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a85b454-27aa-47da-98c8-1360ea8d80a2/OceanDNA-b6783.fa --refList OceanDNA-b6783/target_genomes.txt --output OceanDNA-b6783/fastani_result.tsv --threads 1
[2023-03-18 20:56:23,981] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:23,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:23,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:23,995] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:23,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:56:23,995] [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 antarcticum	strain=DSM 19726	GCA_000419685.1	271155	271155	type	True	80.7791	528	884	95	below_threshold
Flavobacterium tegetincola	strain=DSM 22377	GCA_000425485.1	150172	150172	type	True	80.2189	510	884	95	below_threshold
Flavobacterium soli	strain=DSM 19725	GCA_000422705.1	344881	344881	type	True	78.9132	345	884	95	below_threshold
Flavobacterium hercynium	strain=DSM 18292	GCA_002217285.1	387094	387094	type	True	78.2485	189	884	95	below_threshold
Flavobacterium undicola	strain=BBQ-18	GCA_009909155.2	1932779	1932779	type	True	78.2401	202	884	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.2123	196	884	95	below_threshold
Flavobacterium frigidimaris	strain=DSM 15937	GCA_002217275.1	262320	262320	type	True	78.0908	206	884	95	below_threshold
Flavobacterium saccharophilum	strain=DSM 1811	GCA_900142735.1	29534	29534	type	True	78.0676	215	884	95	below_threshold
Flavobacterium hydatis	strain=DSM 2063	GCA_000737695.1	991	991	type	True	77.9619	213	884	95	below_threshold
Flavobacterium succinicans	strain=DSM 4002	GCA_900114945.1	29536	29536	type	True	77.9316	185	884	95	below_threshold
Flavobacterium succinicans	strain=LMG 10402	GCA_000611675.1	29536	29536	type	True	77.9184	187	884	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	77.9178	230	884	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	77.9123	239	884	95	below_threshold
Flavobacterium hydatis	strain=ATCC 29551	GCA_002217335.1	991	991	type	True	77.8962	218	884	95	below_threshold
Flavobacterium granuli	strain=DSM 19729	GCA_900129705.1	280093	280093	type	True	77.8772	194	884	95	below_threshold
Flavobacterium flevense	strain=NBRC 14960	GCA_006539745.1	983	983	type	True	77.8342	190	884	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	77.8246	193	884	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	77.7963	187	884	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	77.6296	206	884	95	below_threshold
Flavobacterium seoulense	strain=EM1321	GCA_000695795.1	1492738	1492738	type	True	77.5608	216	884	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.5468	215	884	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.4566	204	884	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.2387	166	884	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.1012	171	884	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	76.8162	123	884	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	76.7089	122	884	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:56:23,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6783/tc_result.tsv
[2023-03-18 20:56:23,996] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:23,996] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:23,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/checkm_data
[2023-03-18 20:56:23,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:24,000] [INFO] Task started: CheckM
[2023-03-18 20:56:24,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6783/checkm_input OceanDNA-b6783/checkm_result
[2023-03-18 20:57:10,836] [INFO] Task succeeded: CheckM
[2023-03-18 20:57:10,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:57:10,838] [INFO] ===== Completeness check finished =====
[2023-03-18 20:57:10,838] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:57:10,839] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6783/markers.fasta)
[2023-03-18 20:57:10,839] [INFO] Task started: Blastn
[2023-03-18 20:57:10,839] [INFO] Running command: blastn -query OceanDNA-b6783/markers.fasta -db /var/lib/cwl/stg343fee2f-f851-4d5d-bf93-396e5414c875/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:57:11,705] [INFO] Task succeeded: Blastn
[2023-03-18 20:57:11,706] [INFO] Selected 23 target genomes.
[2023-03-18 20:57:11,706] [INFO] Target genome list was writen to OceanDNA-b6783/target_genomes_gtdb.txt
[2023-03-18 20:57:11,826] [INFO] Task started: fastANI
[2023-03-18 20:57:11,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a85b454-27aa-47da-98c8-1360ea8d80a2/OceanDNA-b6783.fa --refList OceanDNA-b6783/target_genomes_gtdb.txt --output OceanDNA-b6783/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:57:26,876] [INFO] Task succeeded: fastANI
[2023-03-18 20:57:26,889] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:57:26,890] [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_000419685.1	s__Flavobacterium antarcticum	80.7938	526	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425485.1	s__Flavobacterium tegetincola	80.2369	508	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422705.1	s__Flavobacterium soli	78.9193	344	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426145.1	s__Flavobacterium sp000426145	78.3035	214	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909155.2	s__Flavobacterium undicola	78.2401	202	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011751075.1	s__Flavobacterium sp011751075	78.1043	191	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737695.1	s__Flavobacterium hydatis	77.9603	213	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.97	99.97	0.98	0.98	2	-
GCF_009711135.1	s__Flavobacterium sp009711135	77.9443	210	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349195.1	s__Flavobacterium sp004349195	77.9239	237	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000611675.1	s__Flavobacterium succinicans	77.9029	187	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.95	97.95	0.95	0.90	3	-
GCF_900142775.1	s__Flavobacterium flevense	77.8938	198	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900129705.1	s__Flavobacterium granuli	77.8912	192	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903839195.1	s__Flavobacterium sp903839195	77.7475	187	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.63	96.46	0.85	0.82	4	-
GCF_000832125.1	s__Flavobacterium hibernum	77.7452	227	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCF_009764685.1	s__Flavobacterium sp009764685	77.7432	192	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCA_017995345.1	s__Flavobacterium sp017995345	77.7011	198	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.61	99.55	0.85	0.83	4	-
GCF_007109225.1	s__Flavobacterium sp007109225	77.669	165	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688495.1	s__Flavobacterium weaverense	77.6182	205	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695795.1	s__Flavobacterium seoulense	77.5536	216	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483315.1	s__Flavobacterium sp002483315	77.5397	193	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	77.5324	216	884	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	77.4761	153	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352205.1	s__Flavobacterium sp002352205	77.2972	211	884	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:57:26,890] [INFO] GTDB search result was written to OceanDNA-b6783/result_gtdb.tsv
[2023-03-18 20:57:26,890] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:57:26,892] [INFO] DFAST_QC result json was written to OceanDNA-b6783/dqc_result.json
[2023-03-18 20:57:26,893] [INFO] DFAST_QC completed!
[2023-03-18 20:57:26,893] [INFO] Total running time: 0h1m40s