[2023-03-14 11:49:37,366] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:37,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:37,368] [INFO] DQC Reference Directory: /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference
[2023-03-14 11:49:38,962] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:38,963] [INFO] Task started: Prodigal
[2023-03-14 11:49:38,963] [INFO] Running command: cat /var/lib/cwl/stg60c7a439-8459-4ae6-908d-b039082a37c8/OceanDNA-b42807.fa | prodigal -d OceanDNA-b42807/cds.fna -a OceanDNA-b42807/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:51,284] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:51,285] [INFO] Task started: HMMsearch
[2023-03-14 11:49:51,285] [INFO] Running command: hmmsearch --tblout OceanDNA-b42807/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/reference_markers.hmm OceanDNA-b42807/protein.faa > /dev/null
[2023-03-14 11:49:51,458] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:51,458] [INFO] Found 6/6 markers.
[2023-03-14 11:49:51,484] [INFO] Query marker FASTA was written to OceanDNA-b42807/markers.fasta
[2023-03-14 11:49:51,486] [INFO] Task started: Blastn
[2023-03-14 11:49:51,486] [INFO] Running command: blastn -query OceanDNA-b42807/markers.fasta -db /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/reference_markers.fasta -out OceanDNA-b42807/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:52,290] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:52,295] [INFO] Selected 34 target genomes.
[2023-03-14 11:49:52,295] [INFO] Target genome list was writen to OceanDNA-b42807/target_genomes.txt
[2023-03-14 11:49:52,319] [INFO] Task started: fastANI
[2023-03-14 11:49:52,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c7a439-8459-4ae6-908d-b039082a37c8/OceanDNA-b42807.fa --refList OceanDNA-b42807/target_genomes.txt --output OceanDNA-b42807/fastani_result.tsv --threads 1
[2023-03-14 11:50:12,152] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:12,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:50:12,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:50:12,164] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:50:12,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:50:12,164] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.7993	78	667	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.4525	70	667	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.4018	72	667	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.3889	62	667	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.3777	50	667	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.3698	67	667	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	76.3085	53	667	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.1906	77	667	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.1865	74	667	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.1797	73	667	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.1699	61	667	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.9716	52	667	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	75.906	64	667	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	75.9037	72	667	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.7916	51	667	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	75.7885	58	667	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.78	61	667	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.7179	61	667	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	75.6467	55	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:50:12,167] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42807/tc_result.tsv
[2023-03-14 11:50:12,168] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:50:12,168] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:50:12,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/checkm_data
[2023-03-14 11:50:12,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:50:12,175] [INFO] Task started: CheckM
[2023-03-14 11:50:12,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42807/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42807/checkm_input OceanDNA-b42807/checkm_result
[2023-03-14 11:50:46,670] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:46,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:46,722] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:46,722] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:46,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42807/markers.fasta)
[2023-03-14 11:50:46,724] [INFO] Task started: Blastn
[2023-03-14 11:50:46,724] [INFO] Running command: blastn -query OceanDNA-b42807/markers.fasta -db /var/lib/cwl/stgdba16000-9bfa-4ba5-b4bb-a5ec992b4846/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42807/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:48,205] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:48,210] [INFO] Selected 33 target genomes.
[2023-03-14 11:50:48,210] [INFO] Target genome list was writen to OceanDNA-b42807/target_genomes_gtdb.txt
[2023-03-14 11:50:48,532] [INFO] Task started: fastANI
[2023-03-14 11:50:48,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg60c7a439-8459-4ae6-908d-b039082a37c8/OceanDNA-b42807.fa --refList OceanDNA-b42807/target_genomes_gtdb.txt --output OceanDNA-b42807/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:51:05,172] [INFO] Task succeeded: fastANI
[2023-03-14 11:51:05,181] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:51:05,182] [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_011051475.1	s__GCA-2746365 sp011051475	76.6932	52	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__GCA-2746365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.6701	107	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937385.1	s__QNFN01 sp009937385	76.4588	69	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__QNFN01;f__QNFN01;g__QNFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008632335.1	s__Thiohalocapsa marina	76.4018	72	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	76.3793	81	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.3299	76	667	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_900110585.1	s__Aquisalimonas asiatica	76.3085	53	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	76.2615	57	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488295.1	s__GCA-2746365 sp015488295	76.2509	61	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-229;f__SZUA-229;g__GCA-2746365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012044895.1	s__Aquisalimonas sp012044895	76.2065	51	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212015.1	s__28-57-27 sp006212015	76.2033	58	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__Halothiobacillaceae;g__28-57-27	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000365.1	s__Thioalkalivibrio_A denitrificans	76.1962	60	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	75.8885	62	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182095.1	s__Plasticicumulans acidivorans	75.78	61	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550215.1	s__Pelomonas sp003550215	75.6302	51	667	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:51:05,184] [INFO] GTDB search result was written to OceanDNA-b42807/result_gtdb.tsv
[2023-03-14 11:51:05,187] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:51:05,191] [INFO] DFAST_QC result json was written to OceanDNA-b42807/dqc_result.json
[2023-03-14 11:51:05,191] [INFO] DFAST_QC completed!
[2023-03-14 11:51:05,191] [INFO] Total running time: 0h1m28s