[2023-03-18 22:17:12,657] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:17:12,658] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:17:12,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference
[2023-03-18 22:17:13,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:17:13,724] [INFO] Task started: Prodigal
[2023-03-18 22:17:13,724] [INFO] Running command: cat /var/lib/cwl/stg246ac773-83b8-40fa-9bc2-4912a34b9eb1/OceanDNA-b36151.fa | prodigal -d OceanDNA-b36151/cds.fna -a OceanDNA-b36151/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:17:36,778] [INFO] Task succeeded: Prodigal
[2023-03-18 22:17:36,778] [INFO] Task started: HMMsearch
[2023-03-18 22:17:36,778] [INFO] Running command: hmmsearch --tblout OceanDNA-b36151/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/reference_markers.hmm OceanDNA-b36151/protein.faa > /dev/null
[2023-03-18 22:17:36,997] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:17:36,997] [INFO] Found 6/6 markers.
[2023-03-18 22:17:37,019] [INFO] Query marker FASTA was written to OceanDNA-b36151/markers.fasta
[2023-03-18 22:17:37,020] [INFO] Task started: Blastn
[2023-03-18 22:17:37,020] [INFO] Running command: blastn -query OceanDNA-b36151/markers.fasta -db /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/reference_markers.fasta -out OceanDNA-b36151/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:37,861] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:37,862] [INFO] Selected 29 target genomes.
[2023-03-18 22:17:37,863] [INFO] Target genome list was writen to OceanDNA-b36151/target_genomes.txt
[2023-03-18 22:17:37,881] [INFO] Task started: fastANI
[2023-03-18 22:17:37,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg246ac773-83b8-40fa-9bc2-4912a34b9eb1/OceanDNA-b36151.fa --refList OceanDNA-b36151/target_genomes.txt --output OceanDNA-b36151/fastani_result.tsv --threads 1
[2023-03-18 22:17:58,496] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:58,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:17:58,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:17:58,511] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 22:17:58,511] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 22:17:58,511] [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
Oceanococcus atlanticus	strain=22II-S10r2	GCA_002088235.1	1317117	1317117	type	True	98.3718	1100	1177	95	conclusive
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	76.4364	119	1177	95	below_threshold
Abyssibacter profundi	strain=OUC007	GCA_003151135.1	2182787	2182787	type	True	76.4283	110	1177	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	76.4079	64	1177	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	76.2435	128	1177	95	below_threshold
Stenotrophomonas maltophilia	strain=NBRC 14161	GCA_001591205.1	40324	40324	type	True	76.1738	70	1177	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.0566	74	1177	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	75.9998	66	1177	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	75.9646	112	1177	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	75.9492	66	1177	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	75.8858	58	1177	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	75.8408	64	1177	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	75.8324	94	1177	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	75.7849	126	1177	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.7282	71	1177	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.7276	76	1177	95	below_threshold
Pseudomonas extremaustralis		GCA_900625045.1	359110	359110	type	True	75.6508	67	1177	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	75.6365	68	1177	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	75.6305	80	1177	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_900102035.1	359110	359110	type	True	75.6166	67	1177	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	75.505	64	1177	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	75.4234	69	1177	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	75.3735	64	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:17:58,511] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36151/tc_result.tsv
[2023-03-18 22:17:58,512] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:17:58,512] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:17:58,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/checkm_data
[2023-03-18 22:17:58,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:17:58,521] [INFO] Task started: CheckM
[2023-03-18 22:17:58,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36151/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36151/checkm_input OceanDNA-b36151/checkm_result
[2023-03-18 22:18:59,132] [INFO] Task succeeded: CheckM
[2023-03-18 22:18:59,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:18:59,201] [INFO] ===== Completeness check finished =====
[2023-03-18 22:18:59,201] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:18:59,201] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36151/markers.fasta)
[2023-03-18 22:18:59,202] [INFO] Task started: Blastn
[2023-03-18 22:18:59,202] [INFO] Running command: blastn -query OceanDNA-b36151/markers.fasta -db /var/lib/cwl/stg9aaa9dae-724d-45e8-b828-8c6b96add05a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36151/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:19:00,762] [INFO] Task succeeded: Blastn
[2023-03-18 22:19:00,763] [INFO] Selected 29 target genomes.
[2023-03-18 22:19:00,763] [INFO] Target genome list was writen to OceanDNA-b36151/target_genomes_gtdb.txt
[2023-03-18 22:19:00,785] [INFO] Task started: fastANI
[2023-03-18 22:19:00,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg246ac773-83b8-40fa-9bc2-4912a34b9eb1/OceanDNA-b36151.fa --refList OceanDNA-b36151/target_genomes_gtdb.txt --output OceanDNA-b36151/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:19:17,403] [INFO] Task succeeded: fastANI
[2023-03-18 22:19:17,415] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:19:17,416] [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_002088235.1	s__Oceanococcus atlanticus	98.3718	1100	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Oceanococcaceae;g__Oceanococcus	95.0	98.37	98.37	0.93	0.93	2	conclusive
GCA_019192445.1	s__MS8 sp019192445	76.6912	73	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Oceanococcaceae;g__MS8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683405.1	s__GCA-2683405 sp002683405	76.4483	92	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__GCA-2683405	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	76.4364	119	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151135.1	s__Abyssibacter profundi	76.4263	110	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__Abyssibacter	95.0	98.39	98.39	0.93	0.93	2	-
GCF_016613475.2	s__Lysobacter arenosi	76.4079	64	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	76.2629	67	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_013395055.1	s__Pseudomonas_Q sp013395055	76.2508	69	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	76.0566	74	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110585.1	s__Aquisalimonas asiatica	75.9998	66	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	75.9922	66	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	75.9886	89	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_900104805.1	s__Pseudomonas_K oryzae	75.9789	111	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222345.1	s__JAAFAL01 sp018222345	75.9455	79	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__OUC007;g__JAAFAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389055.1	s__Alcanivorax sp002389055	75.9394	56	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCA_003484865.1	s__Stenotrophomonas sp003484865	75.8077	61	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.34	98.34	0.85	0.85	2	-
GCA_002840095.1	s__Sulfurivermis sp002840095	75.7498	86	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431645.1	s__Stenotrophomonas_A panacihumi	75.6607	77	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003402235.1	s__Parahaliea mediterranea	75.6305	80	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717705.1	s__JADKFD01 sp016717705	75.597	71	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483055.1	s__Dokdonella sp002483055	75.59	53	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565625.1	s__Wenzhouxiangella sp003565625	75.5823	58	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003788585.1	s__Salinisphaera japonica	75.5228	63	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:19:17,431] [INFO] GTDB search result was written to OceanDNA-b36151/result_gtdb.tsv
[2023-03-18 22:19:17,431] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:19:17,434] [INFO] DFAST_QC result json was written to OceanDNA-b36151/dqc_result.json
[2023-03-18 22:19:17,434] [INFO] DFAST_QC completed!
[2023-03-18 22:19:17,434] [INFO] Total running time: 0h2m5s