[2023-03-15 16:58:29,344] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:58:29,346] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:58:29,346] [INFO] DQC Reference Directory: /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference
[2023-03-15 16:58:31,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:58:31,347] [INFO] Task started: Prodigal
[2023-03-15 16:58:31,347] [INFO] Running command: cat /var/lib/cwl/stg8bc44016-3cbd-447d-ac1e-9c0b35655c51/OceanDNA-b30707.fa | prodigal -d OceanDNA-b30707/cds.fna -a OceanDNA-b30707/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:58:38,796] [INFO] Task succeeded: Prodigal
[2023-03-15 16:58:38,796] [INFO] Task started: HMMsearch
[2023-03-15 16:58:38,796] [INFO] Running command: hmmsearch --tblout OceanDNA-b30707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/reference_markers.hmm OceanDNA-b30707/protein.faa > /dev/null
[2023-03-15 16:58:38,943] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:58:38,944] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg8bc44016-3cbd-447d-ac1e-9c0b35655c51/OceanDNA-b30707.fa]
[2023-03-15 16:58:38,964] [INFO] Query marker FASTA was written to OceanDNA-b30707/markers.fasta
[2023-03-15 16:58:38,965] [INFO] Task started: Blastn
[2023-03-15 16:58:38,965] [INFO] Running command: blastn -query OceanDNA-b30707/markers.fasta -db /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/reference_markers.fasta -out OceanDNA-b30707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:58:39,552] [INFO] Task succeeded: Blastn
[2023-03-15 16:58:39,558] [INFO] Selected 14 target genomes.
[2023-03-15 16:58:39,558] [INFO] Target genome list was writen to OceanDNA-b30707/target_genomes.txt
[2023-03-15 16:58:39,567] [INFO] Task started: fastANI
[2023-03-15 16:58:39,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc44016-3cbd-447d-ac1e-9c0b35655c51/OceanDNA-b30707.fa --refList OceanDNA-b30707/target_genomes.txt --output OceanDNA-b30707/fastani_result.tsv --threads 1
[2023-03-15 16:58:49,038] [INFO] Task succeeded: fastANI
[2023-03-15 16:58:49,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:58:49,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:58:49,047] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:58:49,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:58:49,048] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.0797	193	313	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4593	165	313	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.4481	146	313	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.1178	164	313	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.0633	167	313	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.0538	159	313	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.0285	165	313	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	77.7912	151	313	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.7162	143	313	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	77.2736	111	313	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.9918	139	313	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.7319	114	313	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.706	97	313	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:58:49,055] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30707/tc_result.tsv
[2023-03-15 16:58:49,067] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:58:49,067] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:58:49,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/checkm_data
[2023-03-15 16:58:49,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:58:49,121] [INFO] Task started: CheckM
[2023-03-15 16:58:49,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30707/checkm_input OceanDNA-b30707/checkm_result
[2023-03-15 16:59:12,935] [INFO] Task succeeded: CheckM
[2023-03-15 16:59:12,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:59:13,080] [INFO] ===== Completeness check finished =====
[2023-03-15 16:59:13,080] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:59:13,081] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30707/markers.fasta)
[2023-03-15 16:59:13,082] [INFO] Task started: Blastn
[2023-03-15 16:59:13,082] [INFO] Running command: blastn -query OceanDNA-b30707/markers.fasta -db /var/lib/cwl/stg9794ac12-0911-4ebf-8ef9-40a6f362ffa0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:59:14,006] [INFO] Task succeeded: Blastn
[2023-03-15 16:59:14,021] [INFO] Selected 15 target genomes.
[2023-03-15 16:59:14,021] [INFO] Target genome list was writen to OceanDNA-b30707/target_genomes_gtdb.txt
[2023-03-15 16:59:14,037] [INFO] Task started: fastANI
[2023-03-15 16:59:14,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bc44016-3cbd-447d-ac1e-9c0b35655c51/OceanDNA-b30707.fa --refList OceanDNA-b30707/target_genomes_gtdb.txt --output OceanDNA-b30707/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:59:23,560] [INFO] Task succeeded: fastANI
[2023-03-15 16:59:23,569] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:59:23,569] [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_011620265.1	s__Albidovulum sp011620265	79.3491	204	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.1767	189	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.9835	200	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	78.9832	181	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	78.7842	172	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	78.475	167	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	78.2869	165	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_003298775.1	s__Rhodosalinus sp003298775	78.1339	154	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314805.1	s__Roseicyclus sp001314805	78.1296	124	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.0727	163	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900177545.1	s__Muriiphilus sp900177545	77.8595	148	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	77.7414	140	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000429765.1	s__Wagnerdoeblera nectariphila	77.4181	134	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	76.9962	103	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	76.9114	116	313	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:59:23,569] [INFO] GTDB search result was written to OceanDNA-b30707/result_gtdb.tsv
[2023-03-15 16:59:23,569] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:59:23,571] [INFO] DFAST_QC result json was written to OceanDNA-b30707/dqc_result.json
[2023-03-15 16:59:23,571] [INFO] DFAST_QC completed!
[2023-03-15 16:59:23,571] [INFO] Total running time: 0h0m54s