[2023-03-15 21:24:36,513] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:36,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:36,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference
[2023-03-15 21:24:37,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:37,630] [INFO] Task started: Prodigal
[2023-03-15 21:24:37,630] [INFO] Running command: cat /var/lib/cwl/stgb305dab9-e918-4496-864e-710f203e6472/OceanDNA-b29386.fa | prodigal -d OceanDNA-b29386/cds.fna -a OceanDNA-b29386/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:24:45,314] [INFO] Task succeeded: Prodigal
[2023-03-15 21:24:45,314] [INFO] Task started: HMMsearch
[2023-03-15 21:24:45,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b29386/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/reference_markers.hmm OceanDNA-b29386/protein.faa > /dev/null
[2023-03-15 21:24:45,478] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:24:45,478] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb305dab9-e918-4496-864e-710f203e6472/OceanDNA-b29386.fa]
[2023-03-15 21:24:45,494] [INFO] Query marker FASTA was written to OceanDNA-b29386/markers.fasta
[2023-03-15 21:24:45,494] [INFO] Task started: Blastn
[2023-03-15 21:24:45,494] [INFO] Running command: blastn -query OceanDNA-b29386/markers.fasta -db /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/reference_markers.fasta -out OceanDNA-b29386/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:24:46,194] [INFO] Task succeeded: Blastn
[2023-03-15 21:24:46,195] [INFO] Selected 18 target genomes.
[2023-03-15 21:24:46,195] [INFO] Target genome list was writen to OceanDNA-b29386/target_genomes.txt
[2023-03-15 21:24:46,206] [INFO] Task started: fastANI
[2023-03-15 21:24:46,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgb305dab9-e918-4496-864e-710f203e6472/OceanDNA-b29386.fa --refList OceanDNA-b29386/target_genomes.txt --output OceanDNA-b29386/fastani_result.tsv --threads 1
[2023-03-15 21:24:56,872] [INFO] Task succeeded: fastANI
[2023-03-15 21:24:56,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:24:56,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:24:56,884] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:24:56,884] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:24:56,884] [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
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	80.2114	254	373	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	79.5482	241	373	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	79.4597	242	373	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.4545	242	373	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	79.0283	212	373	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	79.0069	213	373	95	below_threshold
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	78.4469	197	373	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.3853	203	373	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.2841	197	373	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.9508	162	373	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	77.5944	150	373	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.5528	152	373	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.1675	122	373	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.087	118	373	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.0826	132	373	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.8362	96	373	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6176	98	373	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	76.5265	74	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:24:56,884] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29386/tc_result.tsv
[2023-03-15 21:24:56,884] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:24:56,885] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:24:56,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/checkm_data
[2023-03-15 21:24:56,885] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:24:56,921] [INFO] Task started: CheckM
[2023-03-15 21:24:56,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29386/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29386/checkm_input OceanDNA-b29386/checkm_result
[2023-03-15 21:25:20,882] [INFO] Task succeeded: CheckM
[2023-03-15 21:25:20,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:25:20,905] [INFO] ===== Completeness check finished =====
[2023-03-15 21:25:20,905] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:25:20,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29386/markers.fasta)
[2023-03-15 21:25:20,906] [INFO] Task started: Blastn
[2023-03-15 21:25:20,906] [INFO] Running command: blastn -query OceanDNA-b29386/markers.fasta -db /var/lib/cwl/stgdbe4c168-2f49-4dfc-b8e1-5419b4462d12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29386/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:22,177] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:22,178] [INFO] Selected 14 target genomes.
[2023-03-15 21:25:22,178] [INFO] Target genome list was writen to OceanDNA-b29386/target_genomes_gtdb.txt
[2023-03-15 21:25:22,211] [INFO] Task started: fastANI
[2023-03-15 21:25:22,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgb305dab9-e918-4496-864e-710f203e6472/OceanDNA-b29386.fa --refList OceanDNA-b29386/target_genomes_gtdb.txt --output OceanDNA-b29386/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:25:31,345] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:31,353] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:25:31,354] [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_003340555.1	s__Jannaschia formosa	80.1998	255	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	79.5274	242	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403735.1	s__Jannaschia rubra	79.4397	243	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001408515.1	s__Jannaschia seosinensis	79.3769	216	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.0069	213	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016820245.1	s__Jannaschia sp016820245	78.8603	226	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113875.1	s__Jannaschia pohangensis	78.4469	197	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.0864	173	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.0004	193	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	77.8232	180	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.6545	155	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	77.6119	137	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424695.1	s__Vannielia litorea_A	77.419	109	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	77.3851	145	373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:25:31,354] [INFO] GTDB search result was written to OceanDNA-b29386/result_gtdb.tsv
[2023-03-15 21:25:31,354] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:25:31,356] [INFO] DFAST_QC result json was written to OceanDNA-b29386/dqc_result.json
[2023-03-15 21:25:31,356] [INFO] DFAST_QC completed!
[2023-03-15 21:25:31,356] [INFO] Total running time: 0h0m55s