[2023-03-16 07:55:45,176] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,176] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,309] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stg93db3d39-36d4-49ef-9935-55e9f0fcdb79/OceanDNA-b23901.fa | prodigal -d OceanDNA-b23901/cds.fna -a OceanDNA-b23901/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:05,040] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:05,040] [INFO] Task started: HMMsearch
[2023-03-16 07:56:05,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b23901/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/reference_markers.hmm OceanDNA-b23901/protein.faa > /dev/null
[2023-03-16 07:56:05,233] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:05,234] [INFO] Found 6/6 markers.
[2023-03-16 07:56:05,252] [INFO] Query marker FASTA was written to OceanDNA-b23901/markers.fasta
[2023-03-16 07:56:05,252] [INFO] Task started: Blastn
[2023-03-16 07:56:05,252] [INFO] Running command: blastn -query OceanDNA-b23901/markers.fasta -db /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/reference_markers.fasta -out OceanDNA-b23901/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:06,038] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:06,039] [INFO] Selected 24 target genomes.
[2023-03-16 07:56:06,039] [INFO] Target genome list was writen to OceanDNA-b23901/target_genomes.txt
[2023-03-16 07:56:06,050] [INFO] Task started: fastANI
[2023-03-16 07:56:06,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg93db3d39-36d4-49ef-9935-55e9f0fcdb79/OceanDNA-b23901.fa --refList OceanDNA-b23901/target_genomes.txt --output OceanDNA-b23901/fastani_result.tsv --threads 1
[2023-03-16 07:56:22,735] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:22,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:22,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:22,747] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:22,747] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:22,747] [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
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.7581	298	985	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	77.6898	234	985	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.3149	250	985	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.1372	164	985	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.1208	167	985	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.1208	167	985	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	77.0895	242	985	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.0337	183	985	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.7409	170	985	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.2633	94	985	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9443	50	985	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	75.9296	66	985	95	below_threshold
Bradyrhizobium centrolobii	strain=BR 10245	GCA_001641635.1	1505087	1505087	type	True	75.8946	71	985	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	75.8127	83	985	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.5746	64	985	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	75.5651	83	985	95	below_threshold
Bradyrhizobium altum	strain=Pear77	GCA_020889705.1	1571202	1571202	type	True	75.4578	71	985	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	75.424	76	985	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:22,748] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23901/tc_result.tsv
[2023-03-16 07:56:22,748] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:22,748] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:22,748] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/checkm_data
[2023-03-16 07:56:22,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:22,863] [INFO] Task started: CheckM
[2023-03-16 07:56:22,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23901/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23901/checkm_input OceanDNA-b23901/checkm_result
[2023-03-16 07:57:11,254] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:11,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:11,260] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:11,260] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:11,260] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23901/markers.fasta)
[2023-03-16 07:57:11,261] [INFO] Task started: Blastn
[2023-03-16 07:57:11,261] [INFO] Running command: blastn -query OceanDNA-b23901/markers.fasta -db /var/lib/cwl/stg8911b066-dd31-49e7-96a0-94c5b471270f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23901/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:12,791] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:12,796] [INFO] Selected 21 target genomes.
[2023-03-16 07:57:12,796] [INFO] Target genome list was writen to OceanDNA-b23901/target_genomes_gtdb.txt
[2023-03-16 07:57:13,030] [INFO] Task started: fastANI
[2023-03-16 07:57:13,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg93db3d39-36d4-49ef-9935-55e9f0fcdb79/OceanDNA-b23901.fa --refList OceanDNA-b23901/target_genomes_gtdb.txt --output OceanDNA-b23901/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:57:25,909] [INFO] Task succeeded: fastANI
[2023-03-16 07:57:25,919] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:57:25,919] [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_016124205.1	s__Hyphobacterium sp016124205	78.0728	281	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692855.1	s__Hyphobacterium sp002692855	78.043	353	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCF_003129605.1	s__Hyphobacterium indicum	77.7695	297	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323565.1	s__Hyphobacterium sp014323565	77.7499	287	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124665.1	s__Hyphobacterium sp016124665	77.5901	286	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783385.1	s__Hyphobacterium sp002783385	77.5817	209	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	77.5578	225	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_017642925.1	s__Maricaulis sp017642925	77.4605	244	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	77.3712	230	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	77.1363	166	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002707795.1	s__Maricaulis sp002707795	77.1112	187	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCA_905480005.1	s__Maricaulis sp905480005	77.0949	195	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103475.1	s__Maricaulis salignorans	77.0894	242	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	76.9208	148	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643585.1	s__Maricaulis sp017643585	76.9063	177	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.94	99.90	0.97	0.94	3	-
GCA_017643475.1	s__Maricaulis sp017643475	76.6913	168	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258865.1	s__Rhodoplanes roseus	75.4379	75	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:57:25,919] [INFO] GTDB search result was written to OceanDNA-b23901/result_gtdb.tsv
[2023-03-16 07:57:25,919] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:57:25,921] [INFO] DFAST_QC result json was written to OceanDNA-b23901/dqc_result.json
[2023-03-16 07:57:25,921] [INFO] DFAST_QC completed!
[2023-03-16 07:57:25,922] [INFO] Total running time: 0h1m41s