[2023-03-17 10:16:56,379] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:16:56,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:16:56,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference
[2023-03-17 10:16:57,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:16:57,517] [INFO] Task started: Prodigal
[2023-03-17 10:16:57,518] [INFO] Running command: cat /var/lib/cwl/stgd4901066-e57a-4800-994c-6a4d2d86ec23/OceanDNA-b23952.fa | prodigal -d OceanDNA-b23952/cds.fna -a OceanDNA-b23952/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:17:12,526] [INFO] Task succeeded: Prodigal
[2023-03-17 10:17:12,526] [INFO] Task started: HMMsearch
[2023-03-17 10:17:12,526] [INFO] Running command: hmmsearch --tblout OceanDNA-b23952/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/reference_markers.hmm OceanDNA-b23952/protein.faa > /dev/null
[2023-03-17 10:17:12,719] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:17:12,719] [INFO] Found 6/6 markers.
[2023-03-17 10:17:12,741] [INFO] Query marker FASTA was written to OceanDNA-b23952/markers.fasta
[2023-03-17 10:17:12,742] [INFO] Task started: Blastn
[2023-03-17 10:17:12,743] [INFO] Running command: blastn -query OceanDNA-b23952/markers.fasta -db /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/reference_markers.fasta -out OceanDNA-b23952/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:17:13,610] [INFO] Task succeeded: Blastn
[2023-03-17 10:17:13,611] [INFO] Selected 17 target genomes.
[2023-03-17 10:17:13,611] [INFO] Target genome list was writen to OceanDNA-b23952/target_genomes.txt
[2023-03-17 10:17:13,625] [INFO] Task started: fastANI
[2023-03-17 10:17:13,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4901066-e57a-4800-994c-6a4d2d86ec23/OceanDNA-b23952.fa --refList OceanDNA-b23952/target_genomes.txt --output OceanDNA-b23952/fastani_result.tsv --threads 1
[2023-03-17 10:17:24,188] [INFO] Task succeeded: fastANI
[2023-03-17 10:17:24,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:17:24,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:17:24,199] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:17:24,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:17:24,199] [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 alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	81.6024	563	800	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	80.4887	504	800	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	78.6678	388	800	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	77.9516	258	800	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	77.9353	257	800	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	77.7327	217	800	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	77.72	217	800	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	77.6646	246	800	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.3541	182	800	95	below_threshold
Glycocaulis alkaliphilus	strain=CGMCC 1.12428	GCA_014637625.1	1434191	1434191	type	True	77.1528	168	800	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.3259	92	800	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.0742	135	800	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.0722	135	800	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8929	76	800	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.6351	75	800	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.5418	93	800	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.4606	79	800	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:17:24,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23952/tc_result.tsv
[2023-03-17 10:17:24,200] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:17:24,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:17:24,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/checkm_data
[2023-03-17 10:17:24,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:17:24,206] [INFO] Task started: CheckM
[2023-03-17 10:17:24,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23952/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23952/checkm_input OceanDNA-b23952/checkm_result
[2023-03-17 10:18:04,079] [INFO] Task succeeded: CheckM
[2023-03-17 10:18:04,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 1.91%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:18:04,103] [INFO] ===== Completeness check finished =====
[2023-03-17 10:18:04,103] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:18:04,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23952/markers.fasta)
[2023-03-17 10:18:04,105] [INFO] Task started: Blastn
[2023-03-17 10:18:04,105] [INFO] Running command: blastn -query OceanDNA-b23952/markers.fasta -db /var/lib/cwl/stg983942f3-c2e6-46a1-a881-72d965cbdd20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23952/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:18:05,808] [INFO] Task succeeded: Blastn
[2023-03-17 10:18:05,813] [INFO] Selected 10 target genomes.
[2023-03-17 10:18:05,813] [INFO] Target genome list was writen to OceanDNA-b23952/target_genomes_gtdb.txt
[2023-03-17 10:18:05,846] [INFO] Task started: fastANI
[2023-03-17 10:18:05,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4901066-e57a-4800-994c-6a4d2d86ec23/OceanDNA-b23952.fa --refList OceanDNA-b23952/target_genomes_gtdb.txt --output OceanDNA-b23952/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:18:12,078] [INFO] Task succeeded: fastANI
[2023-03-17 10:18:12,085] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:18:12,085] [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_002707795.1	s__Maricaulis sp002707795	99.4055	583	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	conclusive
GCA_017642925.1	s__Maricaulis sp017642925	93.9908	743	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871165.1	s__Maricaulis sp005871165	81.6281	561	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016817355.1	s__Maricaulis parjimensis	81.2644	542	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694345.1	s__Maricaulis sp002694345	80.9705	381	800	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	80.5894	488	800	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	80.4887	504	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_000014745.1	s__Maricaulis maris_A	80.1429	474	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCA_905480005.1	s__Maricaulis sp905480005	80.135	405	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152745.1	s__Oceanicaulis sp000152745	77.7509	204	800	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	98.46	98.38	0.90	0.88	7	-
--------------------------------------------------------------------------------
[2023-03-17 10:18:12,087] [INFO] GTDB search result was written to OceanDNA-b23952/result_gtdb.tsv
[2023-03-17 10:18:12,091] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:18:12,094] [INFO] DFAST_QC result json was written to OceanDNA-b23952/dqc_result.json
[2023-03-17 10:18:12,094] [INFO] DFAST_QC completed!
[2023-03-17 10:18:12,094] [INFO] Total running time: 0h1m16s