[2023-03-17 05:34:58,188] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,188] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference
[2023-03-17 05:34:59,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,321] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,321] [INFO] Running command: cat /var/lib/cwl/stg12e31ce6-f5f7-46d1-bf92-82fe7e63e0a8/OceanDNA-b41266.fa | prodigal -d OceanDNA-b41266/cds.fna -a OceanDNA-b41266/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:29,628] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:29,629] [INFO] Task started: HMMsearch
[2023-03-17 05:35:29,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b41266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/reference_markers.hmm OceanDNA-b41266/protein.faa > /dev/null
[2023-03-17 05:35:29,845] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:29,846] [INFO] Found 6/6 markers.
[2023-03-17 05:35:29,893] [INFO] Query marker FASTA was written to OceanDNA-b41266/markers.fasta
[2023-03-17 05:35:29,893] [INFO] Task started: Blastn
[2023-03-17 05:35:29,893] [INFO] Running command: blastn -query OceanDNA-b41266/markers.fasta -db /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/reference_markers.fasta -out OceanDNA-b41266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:30,809] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:30,822] [INFO] Selected 20 target genomes.
[2023-03-17 05:35:30,822] [INFO] Target genome list was writen to OceanDNA-b41266/target_genomes.txt
[2023-03-17 05:35:30,836] [INFO] Task started: fastANI
[2023-03-17 05:35:30,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e31ce6-f5f7-46d1-bf92-82fe7e63e0a8/OceanDNA-b41266.fa --refList OceanDNA-b41266/target_genomes.txt --output OceanDNA-b41266/fastani_result.tsv --threads 1
[2023-03-17 05:35:52,952] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:52,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:52,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:52,965] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2023-03-17 05:35:52,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 05:35:52,965] [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
Pseudomonas fulva	strain=DSM 17717	GCA_000621265.1	47880	47880	type	True	99.4784	1336	1485	95	conclusive
Pseudomonas fulva	strain=NBRC 16637	GCA_000730565.1	47880	47880	type	True	99.4768	1334	1485	95	conclusive
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	84.5917	1087	1485	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	84.5557	1078	1485	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	84.5497	1037	1485	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	84.5152	983	1485	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	84.4712	1068	1485	95	below_threshold
Pseudomonas putida	strain=NCTC10936	GCA_900455645.1	303	303	suspected-type	True	84.4309	1085	1485	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	84.4217	1064	1485	95	below_threshold
Pseudomonas putida	strain=NBRC 14164	GCA_000412675.1	303	303	suspected-type	True	84.3573	1082	1485	95	below_threshold
Pseudomonas parafulva	strain=DSM 17004	GCA_000425765.1	157782	157782	suspected-type	True	84.3447	1107	1485	95	below_threshold
Pseudomonas juntendi	strain=BML3	GCA_009932375.1	2666183	2666183	type	True	84.0992	985	1485	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	83.9604	995	1485	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	83.8665	993	1485	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	83.7261	1015	1485	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	83.6972	1057	1485	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	83.6562	1028	1485	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	83.6361	1030	1485	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	83.581	1026	1485	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	83.5137	977	1485	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:35:52,967] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41266/tc_result.tsv
[2023-03-17 05:35:52,971] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:52,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:52,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/checkm_data
[2023-03-17 05:35:52,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:53,045] [INFO] Task started: CheckM
[2023-03-17 05:35:53,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41266/checkm_input OceanDNA-b41266/checkm_result
[2023-03-17 05:37:05,385] [INFO] Task succeeded: CheckM
[2023-03-17 05:37:05,386] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:37:05,433] [INFO] ===== Completeness check finished =====
[2023-03-17 05:37:05,433] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:37:05,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41266/markers.fasta)
[2023-03-17 05:37:05,434] [INFO] Task started: Blastn
[2023-03-17 05:37:05,434] [INFO] Running command: blastn -query OceanDNA-b41266/markers.fasta -db /var/lib/cwl/stg632fdc6a-f52f-410c-86fc-f0fd16bf7753/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:37:07,167] [INFO] Task succeeded: Blastn
[2023-03-17 05:37:07,184] [INFO] Selected 21 target genomes.
[2023-03-17 05:37:07,184] [INFO] Target genome list was writen to OceanDNA-b41266/target_genomes_gtdb.txt
[2023-03-17 05:37:07,449] [INFO] Task started: fastANI
[2023-03-17 05:37:07,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg12e31ce6-f5f7-46d1-bf92-82fe7e63e0a8/OceanDNA-b41266.fa --refList OceanDNA-b41266/target_genomes_gtdb.txt --output OceanDNA-b41266/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:37:31,751] [INFO] Task succeeded: fastANI
[2023-03-17 05:37:31,763] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:37:31,763] [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_000730565.1	s__Pseudomonas_E fulva	99.4768	1334	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.00	95.45	0.93	0.89	89	conclusive
GCF_002021815.1	s__Pseudomonas_E parafulva_B	93.9294	1291	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	97.25	0.94	0.89	23	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	84.7642	1042	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	84.6016	1060	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000730605.1	s__Pseudomonas_E monteilii	84.5659	1076	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	84.5498	1057	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013373935.1	s__Pseudomonas_E sp002438125	84.5085	984	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	-
GCF_015680405.1	s__Pseudomonas_E pudica	84.4405	1061	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_002165135.1	s__Pseudomonas_E sp002165135	84.4325	1044	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412675.1	s__Pseudomonas_E putida	84.3482	1083	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	97.45	0.89	0.83	24	-
GCF_016658545.1	s__Pseudomonas_E sp016658545	84.3367	1046	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	84.2275	1009	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002112505.1	s__Pseudomonas_E sp002112505	84.1496	1072	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_009391885.1	s__Pseudomonas_E sp009391885	84.1264	1024	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932375.1	s__Pseudomonas_E juntendi	84.0845	987	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	97.13	0.84	0.79	41	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	83.9284	1074	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_016648105.1	s__Pseudomonas_E sp016648105	83.9074	1001	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	83.8721	993	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003231305.1	s__Pseudomonas_E sichuanensis	83.735	1014	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	83.456	981	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004357765.1	s__Pseudomonas_E putida_U	83.3831	960	1485	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:37:31,765] [INFO] GTDB search result was written to OceanDNA-b41266/result_gtdb.tsv
[2023-03-17 05:37:31,768] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:37:31,772] [INFO] DFAST_QC result json was written to OceanDNA-b41266/dqc_result.json
[2023-03-17 05:37:31,772] [INFO] DFAST_QC completed!
[2023-03-17 05:37:31,772] [INFO] Total running time: 0h2m34s