[2023-03-16 15:26:08,213] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,213] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference
[2023-03-16 15:26:09,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:09,503] [INFO] Task started: Prodigal
[2023-03-16 15:26:09,504] [INFO] Running command: cat /var/lib/cwl/stg173a6278-b0ac-4e73-9dbe-faea512032df/OceanDNA-b23909.fa | prodigal -d OceanDNA-b23909/cds.fna -a OceanDNA-b23909/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:27,015] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:27,015] [INFO] Task started: HMMsearch
[2023-03-16 15:26:27,016] [INFO] Running command: hmmsearch --tblout OceanDNA-b23909/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/reference_markers.hmm OceanDNA-b23909/protein.faa > /dev/null
[2023-03-16 15:26:27,284] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:27,285] [INFO] Found 6/6 markers.
[2023-03-16 15:26:27,303] [INFO] Query marker FASTA was written to OceanDNA-b23909/markers.fasta
[2023-03-16 15:26:27,303] [INFO] Task started: Blastn
[2023-03-16 15:26:27,303] [INFO] Running command: blastn -query OceanDNA-b23909/markers.fasta -db /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/reference_markers.fasta -out OceanDNA-b23909/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:28,468] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:28,469] [INFO] Selected 22 target genomes.
[2023-03-16 15:26:28,469] [INFO] Target genome list was writen to OceanDNA-b23909/target_genomes.txt
[2023-03-16 15:26:28,478] [INFO] Task started: fastANI
[2023-03-16 15:26:28,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg173a6278-b0ac-4e73-9dbe-faea512032df/OceanDNA-b23909.fa --refList OceanDNA-b23909/target_genomes.txt --output OceanDNA-b23909/fastani_result.tsv --threads 1
[2023-03-16 15:26:48,290] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:48,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:48,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:48,304] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:48,304] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:26:48,304] [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
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	77.5874	190	757	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.5222	224	757	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.2374	190	757	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.1936	199	757	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.1695	198	757	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	77.1467	214	757	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.0458	168	757	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.0458	168	757	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_009806145.1	1133559	1133559	type	True	77.0071	166	757	95	below_threshold
Phenylobacterium glaciei	strain=20VBR1	GCA_016772415.2	2803784	2803784	type	True	76.3597	88	757	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	76.3104	91	757	95	below_threshold
Brevundimonas diminuta	strain=NCTC8545	GCA_900445995.1	293	293	type	True	76.2576	92	757	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.1353	87	757	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	75.9729	69	757	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	75.8857	67	757	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	75.8679	65	757	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	75.8679	65	757	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	75.8518	64	757	95	below_threshold
Methylobacterium haplocladii	strain=DSM 24195	GCA_022179265.1	1176176	1176176	type	True	75.8441	60	757	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	75.821	67	757	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	75.6445	60	757	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	75.6334	63	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:26:48,304] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23909/tc_result.tsv
[2023-03-16 15:26:48,304] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:48,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:48,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/checkm_data
[2023-03-16 15:26:48,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:48,310] [INFO] Task started: CheckM
[2023-03-16 15:26:48,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23909/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23909/checkm_input OceanDNA-b23909/checkm_result
[2023-03-16 15:27:29,177] [INFO] Task succeeded: CheckM
[2023-03-16 15:27:29,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:27:29,179] [INFO] ===== Completeness check finished =====
[2023-03-16 15:27:29,180] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:27:29,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23909/markers.fasta)
[2023-03-16 15:27:29,181] [INFO] Task started: Blastn
[2023-03-16 15:27:29,181] [INFO] Running command: blastn -query OceanDNA-b23909/markers.fasta -db /var/lib/cwl/stgb3abfb52-e4d0-4218-b4d4-a68d9d79fa5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23909/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:27:30,915] [INFO] Task succeeded: Blastn
[2023-03-16 15:27:30,916] [INFO] Selected 18 target genomes.
[2023-03-16 15:27:30,916] [INFO] Target genome list was writen to OceanDNA-b23909/target_genomes_gtdb.txt
[2023-03-16 15:27:31,447] [INFO] Task started: fastANI
[2023-03-16 15:27:31,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg173a6278-b0ac-4e73-9dbe-faea512032df/OceanDNA-b23909.fa --refList OceanDNA-b23909/target_genomes_gtdb.txt --output OceanDNA-b23909/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:27:48,880] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:48,891] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 15:27:48,891] [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_002692855.1	s__Hyphobacterium sp002692855	99.9741	744	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	99.83	99.83	0.96	0.96	2	conclusive
GCA_016124205.1	s__Hyphobacterium sp016124205	82.1603	409	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	77.69	248	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	77.6205	188	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCA_002707795.1	s__Maricaulis sp002707795	77.5327	176	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_003129605.1	s__Hyphobacterium indicum	77.5222	224	757	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	77.3462	202	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	77.1853	144	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323565.1	s__Hyphobacterium sp014323565	77.1786	195	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124675.1	s__Oceanicaulis sp016124675	77.172	133	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	77.1467	214	757	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	77.0651	214	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783385.1	s__Hyphobacterium sp002783385	76.6277	151	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018135625.1	s__BOG-935 sp018135625	76.2609	93	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__BOG-935	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897755.1	s__Afipia sp001897755	76.0668	57	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.98	99.98	0.98	0.98	2	-
GCA_016774605.1	s__Stappia sp016774605	76.0117	58	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012745.1	s__Mesorhizobium_D ephedrae	76.0105	87	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000502835.1	s__Mesorhizobium sp000502835	75.656	70	757	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:27:48,891] [INFO] GTDB search result was written to OceanDNA-b23909/result_gtdb.tsv
[2023-03-16 15:27:48,891] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:27:48,893] [INFO] DFAST_QC result json was written to OceanDNA-b23909/dqc_result.json
[2023-03-16 15:27:48,894] [INFO] DFAST_QC completed!
[2023-03-16 15:27:48,894] [INFO] Total running time: 0h1m41s