[2023-03-15 13:03:53,430] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,430] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,431] [INFO] DQC Reference Directory: /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference
[2023-03-15 13:03:54,658] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,658] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,659] [INFO] Running command: cat /var/lib/cwl/stg8e9eb3dc-f04c-4a38-a2da-9618ecc48f91/OceanDNA-b26809.fa | prodigal -d OceanDNA-b26809/cds.fna -a OceanDNA-b26809/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:16,770] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:16,770] [INFO] Task started: HMMsearch
[2023-03-15 13:04:16,770] [INFO] Running command: hmmsearch --tblout OceanDNA-b26809/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/reference_markers.hmm OceanDNA-b26809/protein.faa > /dev/null
[2023-03-15 13:04:17,036] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:17,037] [INFO] Found 6/6 markers.
[2023-03-15 13:04:17,062] [INFO] Query marker FASTA was written to OceanDNA-b26809/markers.fasta
[2023-03-15 13:04:17,062] [INFO] Task started: Blastn
[2023-03-15 13:04:17,062] [INFO] Running command: blastn -query OceanDNA-b26809/markers.fasta -db /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/reference_markers.fasta -out OceanDNA-b26809/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:17,845] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:17,846] [INFO] Selected 17 target genomes.
[2023-03-15 13:04:17,847] [INFO] Target genome list was writen to OceanDNA-b26809/target_genomes.txt
[2023-03-15 13:04:17,857] [INFO] Task started: fastANI
[2023-03-15 13:04:17,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9eb3dc-f04c-4a38-a2da-9618ecc48f91/OceanDNA-b26809.fa --refList OceanDNA-b26809/target_genomes.txt --output OceanDNA-b26809/fastani_result.tsv --threads 1
[2023-03-15 13:04:33,577] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:33,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:33,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:33,588] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:04:33,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:04:33,588] [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
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	90.2372	936	1209	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	81.1539	683	1209	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_000421645.1	182270	182270	type	True	81.045	710	1209	95	below_threshold
Aurantimonas coralicida	strain=DSM 14790	GCA_001463825.1	182270	182270	type	True	81.0359	705	1209	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.6631	639	1209	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.4487	634	1209	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.3884	639	1209	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.7324	540	1209	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.5718	565	1209	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.2738	540	1209	95	below_threshold
Chelativorans alearense	strain=UJN715	GCA_010993735.1	2681495	2681495	type	True	76.9895	283	1209	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.407	167	1209	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	76.4043	232	1209	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.3621	187	1209	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	75.967	103	1209	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	75.9619	140	1209	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	75.4142	81	1209	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:33,588] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26809/tc_result.tsv
[2023-03-15 13:04:33,588] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:33,588] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:33,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/checkm_data
[2023-03-15 13:04:33,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:33,596] [INFO] Task started: CheckM
[2023-03-15 13:04:33,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26809/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26809/checkm_input OceanDNA-b26809/checkm_result
[2023-03-15 13:05:27,921] [INFO] Task succeeded: CheckM
[2023-03-15 13:05:27,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:05:27,924] [INFO] ===== Completeness check finished =====
[2023-03-15 13:05:27,924] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:05:27,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26809/markers.fasta)
[2023-03-15 13:05:27,926] [INFO] Task started: Blastn
[2023-03-15 13:05:27,926] [INFO] Running command: blastn -query OceanDNA-b26809/markers.fasta -db /var/lib/cwl/stge912e4e3-ab68-467c-8dca-81150fd15299/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26809/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:05:29,340] [INFO] Task succeeded: Blastn
[2023-03-15 13:05:29,341] [INFO] Selected 13 target genomes.
[2023-03-15 13:05:29,341] [INFO] Target genome list was writen to OceanDNA-b26809/target_genomes_gtdb.txt
[2023-03-15 13:05:29,410] [INFO] Task started: fastANI
[2023-03-15 13:05:29,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e9eb3dc-f04c-4a38-a2da-9618ecc48f91/OceanDNA-b26809.fa --refList OceanDNA-b26809/target_genomes_gtdb.txt --output OceanDNA-b26809/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:05:41,518] [INFO] Task succeeded: fastANI
[2023-03-15 13:05:41,527] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:05:41,527] [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_011050685.1	s__Aurantimonas coralicida_A	97.1081	1016	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	99.96	99.96	0.91	0.91	2	conclusive
GCF_017183135.1	s__Aurantimonas sp017183135	90.2313	936	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153465.1	s__Aurantimonas manganoxydans	81.1154	687	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	99.99	99.99	1.00	1.00	2	-
GCF_000421645.1	s__Aurantimonas coralicida	81.0733	707	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_010500835.1	s__Aurantimonas aggregata	80.6822	637	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196845.1	s__Aurantimonas endophytica	80.388	638	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	79.633	599	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	79.5619	566	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	79.274	540	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	76.9975	282	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013459645.1	s__Martelella sp013459645	76.9525	227	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014193695.1	s__Rhizobium sp014193695	76.6169	183	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.81	98.81	0.97	0.97	2	-
GCF_018987265.1	s__Rhizobium sp018987265	76.3752	189	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:05:41,527] [INFO] GTDB search result was written to OceanDNA-b26809/result_gtdb.tsv
[2023-03-15 13:05:41,527] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:05:41,529] [INFO] DFAST_QC result json was written to OceanDNA-b26809/dqc_result.json
[2023-03-15 13:05:41,529] [INFO] DFAST_QC completed!
[2023-03-15 13:05:41,529] [INFO] Total running time: 0h1m48s