[2023-03-18 07:29:29,816] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,816] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference
[2023-03-18 07:29:30,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,929] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,929] [INFO] Running command: cat /var/lib/cwl/stg283158d7-3047-4d97-8fe8-d74aad2854f0/OceanDNA-b35793.fa | prodigal -d OceanDNA-b35793/cds.fna -a OceanDNA-b35793/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:42,409] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:42,410] [INFO] Task started: HMMsearch
[2023-03-18 07:29:42,410] [INFO] Running command: hmmsearch --tblout OceanDNA-b35793/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/reference_markers.hmm OceanDNA-b35793/protein.faa > /dev/null
[2023-03-18 07:29:42,580] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:42,580] [INFO] Found 6/6 markers.
[2023-03-18 07:29:42,594] [INFO] Query marker FASTA was written to OceanDNA-b35793/markers.fasta
[2023-03-18 07:29:42,594] [INFO] Task started: Blastn
[2023-03-18 07:29:42,594] [INFO] Running command: blastn -query OceanDNA-b35793/markers.fasta -db /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/reference_markers.fasta -out OceanDNA-b35793/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:43,341] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:43,342] [INFO] Selected 35 target genomes.
[2023-03-18 07:29:43,343] [INFO] Target genome list was writen to OceanDNA-b35793/target_genomes.txt
[2023-03-18 07:29:43,358] [INFO] Task started: fastANI
[2023-03-18 07:29:43,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg283158d7-3047-4d97-8fe8-d74aad2854f0/OceanDNA-b35793.fa --refList OceanDNA-b35793/target_genomes.txt --output OceanDNA-b35793/fastani_result.tsv --threads 1
[2023-03-18 07:30:03,051] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:03,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:03,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:03,064] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:03,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:03,064] [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	77.2159	100	595	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.7795	68	595	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.4997	90	595	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.4209	88	595	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	76.4045	62	595	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	76.3967	60	595	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.3156	55	595	95	below_threshold
Marichromatium bheemlicum	strain=DSM 18632	GCA_012276755.1	365339	365339	type	True	76.2521	61	595	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2327	65	595	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.1892	52	595	95	below_threshold
Ectothiorhodospira marina	strain=DSM 241	GCA_900109495.1	1396821	1396821	type	True	76.1874	51	595	95	below_threshold
Thermithiobacillus tepidarius	strain=DSM 3134	GCA_000423825.1	929	929	type	True	76.1159	61	595	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.0943	74	595	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.0849	57	595	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.0075	50	595	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	75.9651	54	595	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.9538	72	595	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	75.8719	51	595	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.8521	56	595	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	75.7696	51	595	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	75.3931	57	595	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:03,064] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35793/tc_result.tsv
[2023-03-18 07:30:03,064] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:03,064] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:03,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/checkm_data
[2023-03-18 07:30:03,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:03,068] [INFO] Task started: CheckM
[2023-03-18 07:30:03,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35793/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35793/checkm_input OceanDNA-b35793/checkm_result
[2023-03-18 07:30:35,174] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:35,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:35,176] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:35,176] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:35,176] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35793/markers.fasta)
[2023-03-18 07:30:35,176] [INFO] Task started: Blastn
[2023-03-18 07:30:35,177] [INFO] Running command: blastn -query OceanDNA-b35793/markers.fasta -db /var/lib/cwl/stg321aff42-ad1b-4059-a86e-a78a44455377/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35793/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:36,597] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:36,598] [INFO] Selected 35 target genomes.
[2023-03-18 07:30:36,598] [INFO] Target genome list was writen to OceanDNA-b35793/target_genomes_gtdb.txt
[2023-03-18 07:30:37,085] [INFO] Task started: fastANI
[2023-03-18 07:30:37,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg283158d7-3047-4d97-8fe8-d74aad2854f0/OceanDNA-b35793.fa --refList OceanDNA-b35793/target_genomes_gtdb.txt --output OceanDNA-b35793/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:56,559] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:56,573] [INFO] Found 26 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:56,574] [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_011371455.1	s__DRQN01 sp011371455	77.5226	60	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.1884	101	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699185.1	s__Thiohalobacter sp002699185	77.05	63	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377945.1	s__Thioalkalivibrio_A sulfidiphilus_A	77.0482	102	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.7757	84	595	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	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.768	105	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_003695825.1	s__J048 sp003695825	76.6931	57	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696465.1	s__J044 sp003696465	76.6104	50	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	76.5451	89	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	76.5392	78	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	76.4997	90	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.4004	89	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012044895.1	s__Aquisalimonas sp012044895	76.2672	61	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	76.2327	65	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCA_016699715.1	s__Competibacter sp016699715	76.2181	51	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	76.0943	74	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	75.9996	62	595	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_900110585.1	s__Aquisalimonas asiatica	75.9954	53	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.9851	72	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	75.9846	71	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	75.8719	51	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_000377405.1	s__Thioalkalivibrio sp000377405	75.8666	50	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.90	97.79	0.93	0.92	11	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	75.7798	67	595	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_003989065.1	s__RXIW01 sp003989065	75.7736	61	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__RXIW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	75.575	54	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_013407925.2	s__Pseudomonas_E fluorescens_AP	75.3017	53	595	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:56,574] [INFO] GTDB search result was written to OceanDNA-b35793/result_gtdb.tsv
[2023-03-18 07:30:56,574] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:56,576] [INFO] DFAST_QC result json was written to OceanDNA-b35793/dqc_result.json
[2023-03-18 07:30:56,577] [INFO] DFAST_QC completed!
[2023-03-18 07:30:56,577] [INFO] Total running time: 0h1m27s