[2023-03-17 13:01:51,454] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,454] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference
[2023-03-17 13:01:52,696] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,696] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,696] [INFO] Running command: cat /var/lib/cwl/stgcc38d6c9-9b25-4562-8ef3-bbec84cde7eb/OceanDNA-b29530.fa | prodigal -d OceanDNA-b29530/cds.fna -a OceanDNA-b29530/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:14,566] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:14,566] [INFO] Task started: HMMsearch
[2023-03-17 13:02:14,566] [INFO] Running command: hmmsearch --tblout OceanDNA-b29530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/reference_markers.hmm OceanDNA-b29530/protein.faa > /dev/null
[2023-03-17 13:02:14,878] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:14,878] [INFO] Found 6/6 markers.
[2023-03-17 13:02:14,904] [INFO] Query marker FASTA was written to OceanDNA-b29530/markers.fasta
[2023-03-17 13:02:14,905] [INFO] Task started: Blastn
[2023-03-17 13:02:14,905] [INFO] Running command: blastn -query OceanDNA-b29530/markers.fasta -db /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/reference_markers.fasta -out OceanDNA-b29530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:15,685] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:15,686] [INFO] Selected 23 target genomes.
[2023-03-17 13:02:15,687] [INFO] Target genome list was writen to OceanDNA-b29530/target_genomes.txt
[2023-03-17 13:02:15,699] [INFO] Task started: fastANI
[2023-03-17 13:02:15,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc38d6c9-9b25-4562-8ef3-bbec84cde7eb/OceanDNA-b29530.fa --refList OceanDNA-b29530/target_genomes.txt --output OceanDNA-b29530/fastani_result.tsv --threads 1
[2023-03-17 13:02:33,666] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:33,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:33,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:33,680] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:33,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:33,680] [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
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	80.754	673	1169	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	80.708	676	1169	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	80.705	683	1169	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	80.2595	607	1169	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	79.3958	366	1169	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.267	416	1169	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.242	416	1169	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.3569	438	1169	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.2202	315	1169	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9512	309	1169	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.9395	355	1169	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.8888	296	1169	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7559	280	1169	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.7444	281	1169	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.64	293	1169	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	77.5475	287	1169	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.4766	276	1169	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	77.4665	263	1169	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	77.4281	275	1169	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.4261	269	1169	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.3815	262	1169	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.2818	263	1169	95	below_threshold
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.3387	129	1169	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:33,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29530/tc_result.tsv
[2023-03-17 13:02:33,680] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:33,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:33,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/checkm_data
[2023-03-17 13:02:33,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:33,688] [INFO] Task started: CheckM
[2023-03-17 13:02:33,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29530/checkm_input OceanDNA-b29530/checkm_result
[2023-03-17 13:03:28,171] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:28,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:28,174] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:28,174] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:28,174] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29530/markers.fasta)
[2023-03-17 13:03:28,175] [INFO] Task started: Blastn
[2023-03-17 13:03:28,175] [INFO] Running command: blastn -query OceanDNA-b29530/markers.fasta -db /var/lib/cwl/stg9f8ed0fe-64b9-49cf-97f2-cb50c02008c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:29,463] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:29,464] [INFO] Selected 16 target genomes.
[2023-03-17 13:03:29,464] [INFO] Target genome list was writen to OceanDNA-b29530/target_genomes_gtdb.txt
[2023-03-17 13:03:29,743] [INFO] Task started: fastANI
[2023-03-17 13:03:29,743] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc38d6c9-9b25-4562-8ef3-bbec84cde7eb/OceanDNA-b29530.fa --refList OceanDNA-b29530/target_genomes_gtdb.txt --output OceanDNA-b29530/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:43,421] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:43,431] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:03:43,431] [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_001626765.1	s__Maritimibacter sp001626765	99.8956	1088	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.88	99.88	0.89	0.89	2	conclusive
GCF_019218295.1	s__Maritimibacter sp019218295	84.1165	807	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152805.1	s__Maritimibacter alkaliphilus	80.7082	676	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCF_009882975.1	s__Maritimibacter harenae	80.281	605	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	79.9455	541	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695005.1	s__Maritimibacter sp002695005	79.8708	613	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	79.2424	416	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	79.0851	424	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520545.1	s__Maritimibacter sp003520545	79.0113	421	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389895.1	s__Maritimibacter sp011389895	78.6751	466	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.1843	349	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177545.1	s__Muriiphilus sp900177545	78.033	369	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	77.9156	352	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCA_006226775.1	s__Marinovum sp006226775	77.8702	358	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	77.7485	373	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	77.5257	289	1169	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:43,431] [INFO] GTDB search result was written to OceanDNA-b29530/result_gtdb.tsv
[2023-03-17 13:03:43,431] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:43,433] [INFO] DFAST_QC result json was written to OceanDNA-b29530/dqc_result.json
[2023-03-17 13:03:43,433] [INFO] DFAST_QC completed!
[2023-03-17 13:03:43,433] [INFO] Total running time: 0h1m52s