[2023-03-16 11:12:57,627] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:12:57,628] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:12:57,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference
[2023-03-16 11:12:58,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:12:58,915] [INFO] Task started: Prodigal
[2023-03-16 11:12:58,915] [INFO] Running command: cat /var/lib/cwl/stgefcdf9b2-8bf6-4d04-969e-446ca3b5d51a/OceanDNA-b38204.fa | prodigal -d OceanDNA-b38204/cds.fna -a OceanDNA-b38204/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:13:30,428] [INFO] Task succeeded: Prodigal
[2023-03-16 11:13:30,429] [INFO] Task started: HMMsearch
[2023-03-16 11:13:30,429] [INFO] Running command: hmmsearch --tblout OceanDNA-b38204/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/reference_markers.hmm OceanDNA-b38204/protein.faa > /dev/null
[2023-03-16 11:13:30,637] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:13:30,638] [INFO] Found 6/6 markers.
[2023-03-16 11:13:30,667] [INFO] Query marker FASTA was written to OceanDNA-b38204/markers.fasta
[2023-03-16 11:13:30,668] [INFO] Task started: Blastn
[2023-03-16 11:13:30,668] [INFO] Running command: blastn -query OceanDNA-b38204/markers.fasta -db /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/reference_markers.fasta -out OceanDNA-b38204/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:13:31,492] [INFO] Task succeeded: Blastn
[2023-03-16 11:13:31,493] [INFO] Selected 24 target genomes.
[2023-03-16 11:13:31,493] [INFO] Target genome list was writen to OceanDNA-b38204/target_genomes.txt
[2023-03-16 11:13:31,533] [INFO] Task started: fastANI
[2023-03-16 11:13:31,533] [INFO] Running command: fastANI --query /var/lib/cwl/stgefcdf9b2-8bf6-4d04-969e-446ca3b5d51a/OceanDNA-b38204.fa --refList OceanDNA-b38204/target_genomes.txt --output OceanDNA-b38204/fastani_result.tsv --threads 1
[2023-03-16 11:13:49,815] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:49,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:13:49,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:13:49,829] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:13:49,829] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:13:49,830] [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
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	88.7267	1138	1307	95	below_threshold
Cobetia crustatorum	strain=JO1	GCA_000591415.1	553385	553385	type	True	84.3126	925	1307	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.7782	476	1307	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.7362	498	1307	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.4979	482	1307	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.2856	422	1307	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	79.1295	436	1307	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	79.0529	447	1307	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	79.0407	459	1307	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	79.0283	405	1307	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	79.0279	430	1307	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.0264	396	1307	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.0182	403	1307	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	79.0015	406	1307	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.9942	445	1307	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	78.9025	432	1307	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.892	397	1307	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.8833	453	1307	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.7537	387	1307	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.662	380	1307	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	78.4009	333	1307	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	78.3433	384	1307	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	78.1321	286	1307	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	78.1273	287	1307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:13:49,830] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38204/tc_result.tsv
[2023-03-16 11:13:49,830] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:13:49,830] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:13:49,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/checkm_data
[2023-03-16 11:13:49,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:13:49,836] [INFO] Task started: CheckM
[2023-03-16 11:13:49,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38204/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38204/checkm_input OceanDNA-b38204/checkm_result
[2023-03-16 11:15:22,647] [INFO] Task succeeded: CheckM
[2023-03-16 11:15:22,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:15:22,653] [INFO] ===== Completeness check finished =====
[2023-03-16 11:15:22,653] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:15:22,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38204/markers.fasta)
[2023-03-16 11:15:22,685] [INFO] Task started: Blastn
[2023-03-16 11:15:22,686] [INFO] Running command: blastn -query OceanDNA-b38204/markers.fasta -db /var/lib/cwl/stg67e97058-9d65-4e6f-ab31-6b023d91695b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38204/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:15:24,323] [INFO] Task succeeded: Blastn
[2023-03-16 11:15:24,325] [INFO] Selected 11 target genomes.
[2023-03-16 11:15:24,325] [INFO] Target genome list was writen to OceanDNA-b38204/target_genomes_gtdb.txt
[2023-03-16 11:15:24,348] [INFO] Task started: fastANI
[2023-03-16 11:15:24,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgefcdf9b2-8bf6-4d04-969e-446ca3b5d51a/OceanDNA-b38204.fa --refList OceanDNA-b38204/target_genomes_gtdb.txt --output OceanDNA-b38204/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:15:33,376] [INFO] Task succeeded: fastANI
[2023-03-16 11:15:33,383] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:15:33,383] [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_000754225.1	s__Cobetia amphilecti	97.0649	1150	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	conclusive
GCF_001720485.1	s__Cobetia marina	88.7344	1137	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	-
GCF_000591415.1	s__Cobetia crustatorum	84.2969	926	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.71	98.71	0.93	0.93	2	-
GCF_009796845.1	s__Cobetia sp009796845	83.1392	979	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	79.7253	499	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCA_001577635.1	s__Halomonas_C sp001577635	79.5296	455	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993675.1	s__Halomonas_C sp010993675	79.5248	463	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	79.4922	483	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	79.2844	422	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	79.2834	472	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	79.1109	467	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:15:33,384] [INFO] GTDB search result was written to OceanDNA-b38204/result_gtdb.tsv
[2023-03-16 11:15:33,384] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:15:33,387] [INFO] DFAST_QC result json was written to OceanDNA-b38204/dqc_result.json
[2023-03-16 11:15:33,387] [INFO] DFAST_QC completed!
[2023-03-16 11:15:33,387] [INFO] Total running time: 0h2m36s