[2023-03-15 11:36:00,595] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:36:00,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:36:00,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference
[2023-03-15 11:36:02,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:36:02,577] [INFO] Task started: Prodigal
[2023-03-15 11:36:02,577] [INFO] Running command: cat /var/lib/cwl/stge5722d23-04ce-4e04-950f-31261d119253/OceanDNA-b38354.fa | prodigal -d OceanDNA-b38354/cds.fna -a OceanDNA-b38354/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:36:16,474] [INFO] Task succeeded: Prodigal
[2023-03-15 11:36:16,474] [INFO] Task started: HMMsearch
[2023-03-15 11:36:16,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b38354/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/reference_markers.hmm OceanDNA-b38354/protein.faa > /dev/null
[2023-03-15 11:36:16,691] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:36:16,691] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5722d23-04ce-4e04-950f-31261d119253/OceanDNA-b38354.fa]
[2023-03-15 11:36:16,760] [INFO] Query marker FASTA was written to OceanDNA-b38354/markers.fasta
[2023-03-15 11:36:16,761] [INFO] Task started: Blastn
[2023-03-15 11:36:16,761] [INFO] Running command: blastn -query OceanDNA-b38354/markers.fasta -db /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/reference_markers.fasta -out OceanDNA-b38354/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:17,505] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:17,515] [INFO] Selected 23 target genomes.
[2023-03-15 11:36:17,516] [INFO] Target genome list was writen to OceanDNA-b38354/target_genomes.txt
[2023-03-15 11:36:17,528] [INFO] Task started: fastANI
[2023-03-15 11:36:17,528] [INFO] Running command: fastANI --query /var/lib/cwl/stge5722d23-04ce-4e04-950f-31261d119253/OceanDNA-b38354.fa --refList OceanDNA-b38354/target_genomes.txt --output OceanDNA-b38354/fastani_result.tsv --threads 1
[2023-03-15 11:36:33,654] [INFO] Task succeeded: fastANI
[2023-03-15 11:36:33,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:36:33,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:36:33,668] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:36:33,668] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:36:33,668] [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
Salinicola salarius	strain=DSM 18044	GCA_003206135.1	430457	430457	type	True	94.7117	594	662	95	below_threshold
Salinicola socius	strain=DSM 19940	GCA_003206115.1	404433	404433	type	True	85.5792	541	662	95	below_threshold
Salinicola socius	strain=SMB35	GCA_001937195.1	404433	404433	type	True	85.5555	539	662	95	below_threshold
Salinicola halophyticus	strain=CR45	GCA_003206695.1	1808881	1808881	type	True	84.7803	529	662	95	below_threshold
Salinicola lusitanus	strain=CR50	GCA_003206045.1	1949085	1949085	type	True	84.3983	546	662	95	below_threshold
Salinicola acroporae	strain=LMG 28587	GCA_003206615.1	1541440	1541440	type	True	84.118	536	662	95	below_threshold
Salinicola halimionae	strain=CPA60	GCA_003206065.1	1949081	1949081	type	True	83.9868	520	662	95	below_threshold
Salinicola peritrichatus	strain=JCM 18795	GCA_003206715.1	1267424	1267424	type	True	83.5624	513	662	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	81.6778	468	662	95	below_threshold
Salinicola tamaricis	strain=F01	GCA_003006155.1	1771309	1771309	type	True	81.5938	459	662	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.8868	232	662	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.8444	270	662	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	78.7995	279	662	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.7986	253	662	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.7552	266	662	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	78.4013	214	662	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.358	248	662	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.1959	205	662	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.1869	237	662	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	78.1318	172	662	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_003028575.1	1684789	1684789	type	True	78.0557	193	662	95	below_threshold
Halomonas urumqiensis	strain=BZ-SZ-XJ27	GCA_002879635.1	1684789	1684789	type	True	78.0072	195	662	95	below_threshold
Halomonas halodenitrificans	strain=DSM 735	GCA_000620045.1	28252	28252	type	True	77.8531	172	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:36:33,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38354/tc_result.tsv
[2023-03-15 11:36:33,680] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:36:33,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:36:33,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/checkm_data
[2023-03-15 11:36:33,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:36:33,777] [INFO] Task started: CheckM
[2023-03-15 11:36:33,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38354/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38354/checkm_input OceanDNA-b38354/checkm_result
[2023-03-15 11:37:12,102] [INFO] Task succeeded: CheckM
[2023-03-15 11:37:12,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.81%
Contamintation: 13.54%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 11:37:12,274] [INFO] ===== Completeness check finished =====
[2023-03-15 11:37:12,274] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:37:12,274] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38354/markers.fasta)
[2023-03-15 11:37:12,275] [INFO] Task started: Blastn
[2023-03-15 11:37:12,275] [INFO] Running command: blastn -query OceanDNA-b38354/markers.fasta -db /var/lib/cwl/stg342c6c9c-eeef-478c-bc29-42d28cb11b26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38354/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:37:13,472] [INFO] Task succeeded: Blastn
[2023-03-15 11:37:13,482] [INFO] Selected 10 target genomes.
[2023-03-15 11:37:13,482] [INFO] Target genome list was writen to OceanDNA-b38354/target_genomes_gtdb.txt
[2023-03-15 11:37:13,493] [INFO] Task started: fastANI
[2023-03-15 11:37:13,493] [INFO] Running command: fastANI --query /var/lib/cwl/stge5722d23-04ce-4e04-950f-31261d119253/OceanDNA-b38354.fa --refList OceanDNA-b38354/target_genomes_gtdb.txt --output OceanDNA-b38354/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:37:21,604] [INFO] Task succeeded: fastANI
[2023-03-15 11:37:21,611] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:37:21,611] [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_002179555.1	s__Salinicola salarius_A	98.0655	632	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003206135.1	s__Salinicola salarius	94.7117	594	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.80	97.80	0.89	0.89	2	-
GCF_001937195.1	s__Salinicola socius	85.5555	539	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	99.48	98.96	0.96	0.93	3	-
GCA_002695065.1	s__Salinicola sp002695065	85.2622	519	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.83	97.83	0.85	0.85	2	-
GCF_008298015.1	s__Salinicola sp008298015	84.9588	531	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206695.1	s__Salinicola halophyticus	84.7911	528	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	97.72	97.72	0.93	0.93	2	-
GCF_003206045.1	s__Salinicola lusitanus	84.3851	546	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	96.87	96.87	0.93	0.93	2	-
GCF_003206715.1	s__Salinicola peritrichatus	83.5757	512	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	80.8354	452	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003206645.1	s__Salinicola aestuarinus	80.2205	383	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:37:21,615] [INFO] GTDB search result was written to OceanDNA-b38354/result_gtdb.tsv
[2023-03-15 11:37:21,622] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:37:21,630] [INFO] DFAST_QC result json was written to OceanDNA-b38354/dqc_result.json
[2023-03-15 11:37:21,630] [INFO] DFAST_QC completed!
[2023-03-15 11:37:21,630] [INFO] Total running time: 0h1m21s