[2023-03-17 07:28:30,371] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:30,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:30,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference
[2023-03-17 07:28:31,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:31,524] [INFO] Task started: Prodigal
[2023-03-17 07:28:31,524] [INFO] Running command: cat /var/lib/cwl/stg9ffe7987-623e-4430-968d-08def32756ae/OceanDNA-b385.fa | prodigal -d OceanDNA-b385/cds.fna -a OceanDNA-b385/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:40,763] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:40,763] [INFO] Task started: HMMsearch
[2023-03-17 07:28:40,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b385/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/reference_markers.hmm OceanDNA-b385/protein.faa > /dev/null
[2023-03-17 07:28:40,912] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:40,912] [INFO] Found 6/6 markers.
[2023-03-17 07:28:40,926] [INFO] Query marker FASTA was written to OceanDNA-b385/markers.fasta
[2023-03-17 07:28:40,926] [INFO] Task started: Blastn
[2023-03-17 07:28:40,926] [INFO] Running command: blastn -query OceanDNA-b385/markers.fasta -db /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/reference_markers.fasta -out OceanDNA-b385/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:41,788] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:41,789] [INFO] Selected 19 target genomes.
[2023-03-17 07:28:41,789] [INFO] Target genome list was writen to OceanDNA-b385/target_genomes.txt
[2023-03-17 07:28:41,797] [INFO] Task started: fastANI
[2023-03-17 07:28:41,797] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ffe7987-623e-4430-968d-08def32756ae/OceanDNA-b385.fa --refList OceanDNA-b385/target_genomes.txt --output OceanDNA-b385/fastani_result.tsv --threads 1
[2023-03-17 07:28:54,346] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:54,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:54,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:54,355] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:54,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:28:54,355] [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
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.9923	204	460	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.2377	133	460	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.1237	165	460	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.8482	145	460	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.6782	107	460	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6063	113	460	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.0962	79	460	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	75.4672	77	460	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	75.4047	53	460	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	75.3838	81	460	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	75.3681	55	460	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	75.2434	62	460	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.2417	62	460	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.1156	69	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:28:54,356] [INFO] DFAST Taxonomy check result was written to OceanDNA-b385/tc_result.tsv
[2023-03-17 07:28:54,356] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:54,356] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:54,356] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/checkm_data
[2023-03-17 07:28:54,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:54,360] [INFO] Task started: CheckM
[2023-03-17 07:28:54,360] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b385/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b385/checkm_input OceanDNA-b385/checkm_result
[2023-03-17 07:29:21,922] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:21,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:21,924] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:21,924] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:21,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b385/markers.fasta)
[2023-03-17 07:29:21,924] [INFO] Task started: Blastn
[2023-03-17 07:29:21,924] [INFO] Running command: blastn -query OceanDNA-b385/markers.fasta -db /var/lib/cwl/stg4a8ef3e8-972e-47a7-8b92-e2e1c392c29d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b385/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:23,381] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:23,382] [INFO] Selected 16 target genomes.
[2023-03-17 07:29:23,382] [INFO] Target genome list was writen to OceanDNA-b385/target_genomes_gtdb.txt
[2023-03-17 07:29:23,595] [INFO] Task started: fastANI
[2023-03-17 07:29:23,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ffe7987-623e-4430-968d-08def32756ae/OceanDNA-b385.fa --refList OceanDNA-b385/target_genomes_gtdb.txt --output OceanDNA-b385/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:31,294] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:31,303] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:31,303] [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_010024485.1	s__Casp-actino5 sp010024485	97.4137	257	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	conclusive
GCA_017859785.1	s__Casp-actino5 sp017859785	81.9479	353	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.23	98.27	0.91	0.86	15	-
GCA_009924875.1	s__Casp-actino5 sp009924875	81.3279	152	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	78.1147	183	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.9753	205	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859395.1	s__Casp-actino5 sp017859395	77.8782	113	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	99.27	98.20	0.94	0.88	4	-
GCA_009923855.1	s__Casp-actino5 sp009923855	77.8456	99	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.6744	169	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.6286	147	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013811855.1	s__JACCUL01 sp013811855	77.4147	124	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACCUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.2663	133	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.0019	118	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	76.8646	144	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009702045.1	s__UBA668 sp009702045	76.8432	110	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.96	99.94	0.98	0.97	6	-
GCA_012730075.1	s__JAAYBP01 sp012730075	76.1264	91	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255565.1	s__RAAP-2 sp002255565	75.954	50	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:31,304] [INFO] GTDB search result was written to OceanDNA-b385/result_gtdb.tsv
[2023-03-17 07:29:31,304] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:31,305] [INFO] DFAST_QC result json was written to OceanDNA-b385/dqc_result.json
[2023-03-17 07:29:31,305] [INFO] DFAST_QC completed!
[2023-03-17 07:29:31,305] [INFO] Total running time: 0h1m1s