[2023-03-16 07:55:45,164] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,165] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stgedd7c701-44d9-4df8-8163-ada0f7c7d691/OceanDNA-b23976.fa | prodigal -d OceanDNA-b23976/cds.fna -a OceanDNA-b23976/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:04,695] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:04,695] [INFO] Task started: HMMsearch
[2023-03-16 07:56:04,695] [INFO] Running command: hmmsearch --tblout OceanDNA-b23976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/reference_markers.hmm OceanDNA-b23976/protein.faa > /dev/null
[2023-03-16 07:56:04,893] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:04,893] [INFO] Found 6/6 markers.
[2023-03-16 07:56:04,911] [INFO] Query marker FASTA was written to OceanDNA-b23976/markers.fasta
[2023-03-16 07:56:04,912] [INFO] Task started: Blastn
[2023-03-16 07:56:04,912] [INFO] Running command: blastn -query OceanDNA-b23976/markers.fasta -db /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/reference_markers.fasta -out OceanDNA-b23976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:05,689] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:05,690] [INFO] Selected 21 target genomes.
[2023-03-16 07:56:05,690] [INFO] Target genome list was writen to OceanDNA-b23976/target_genomes.txt
[2023-03-16 07:56:05,703] [INFO] Task started: fastANI
[2023-03-16 07:56:05,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd7c701-44d9-4df8-8163-ada0f7c7d691/OceanDNA-b23976.fa --refList OceanDNA-b23976/target_genomes.txt --output OceanDNA-b23976/fastani_result.tsv --threads 1
[2023-03-16 07:56:17,807] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:17,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:17,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:17,820] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:56:17,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:56:17,827] [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
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.7505	280	985	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.722	285	985	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.71	286	985	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.6276	282	985	95	below_threshold
Glycocaulis alkaliphilus	strain=6B-8	GCA_004000605.1	1434191	1434191	type	True	77.6069	294	985	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.5499	282	985	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.4334	329	985	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.3992	328	985	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.149	196	985	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.4897	97	985	95	below_threshold
Phenylobacterium soli	strain=LX32	GCA_003254475.1	2170551	2170551	type	True	76.4642	94	985	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	76.4238	61	985	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	76.2401	89	985	95	below_threshold
Brevundimonas bullata	strain=HAMBI_262	GCA_003350205.1	13160	13160	type	True	76.2225	105	985	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	76.0687	76	985	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	76.0626	72	985	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	76.0046	72	985	95	below_threshold
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	75.9075	79	985	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.8694	78	985	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.8042	82	985	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:17,827] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23976/tc_result.tsv
[2023-03-16 07:56:17,828] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:17,828] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:17,828] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/checkm_data
[2023-03-16 07:56:17,828] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:18,070] [INFO] Task started: CheckM
[2023-03-16 07:56:18,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23976/checkm_input OceanDNA-b23976/checkm_result
[2023-03-16 07:57:05,536] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:05,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:05,550] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:05,550] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:05,550] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23976/markers.fasta)
[2023-03-16 07:57:05,551] [INFO] Task started: Blastn
[2023-03-16 07:57:05,551] [INFO] Running command: blastn -query OceanDNA-b23976/markers.fasta -db /var/lib/cwl/stg3c29cf43-745e-4b72-891f-7bb716df7ed9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:06,798] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:06,799] [INFO] Selected 10 target genomes.
[2023-03-16 07:57:06,799] [INFO] Target genome list was writen to OceanDNA-b23976/target_genomes_gtdb.txt
[2023-03-16 07:57:06,986] [INFO] Task started: fastANI
[2023-03-16 07:57:06,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd7c701-44d9-4df8-8163-ada0f7c7d691/OceanDNA-b23976.fa --refList OceanDNA-b23976/target_genomes_gtdb.txt --output OceanDNA-b23976/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:57:12,810] [INFO] Task succeeded: fastANI
[2023-03-16 07:57:12,817] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:57:12,817] [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_000152745.1	s__Oceanicaulis sp000152745	86.6227	835	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
GCF_000420265.1	s__Oceanicaulis alexandrii	84.0555	770	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	97.56	97.05	0.94	0.85	5	-
GCF_003046365.1	s__Oceanicaulis sp003046365	83.745	758	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	96.56	96.56	0.93	0.93	2	-
GCF_008630495.1	s__Oceanicaulis satelles	78.5686	377	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050995.1	s__Glycocaulis profundi	78.2379	327	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Glycocaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	78.1594	386	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_001657295.1	s__Oceanicaulis sp001657295	78.1079	372	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793635.1	s__Marinicauda pacifica	77.722	285	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003122085.1	s__WD6-1 sp003122085	77.5606	281	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571185.1	s__Oceanicaulis sp007571185	77.2483	131	985	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	99.03	99.03	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:57:12,827] [INFO] GTDB search result was written to OceanDNA-b23976/result_gtdb.tsv
[2023-03-16 07:57:12,831] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:57:12,832] [INFO] DFAST_QC result json was written to OceanDNA-b23976/dqc_result.json
[2023-03-16 07:57:12,832] [INFO] DFAST_QC completed!
[2023-03-16 07:57:12,833] [INFO] Total running time: 0h1m28s