[2023-03-18 21:15:29,378] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,379] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,379] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference
[2023-03-18 21:15:31,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,043] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,043] [INFO] Running command: cat /var/lib/cwl/stg03cf10f8-a52d-4c36-acf4-a2b9ecf0d08f/OceanDNA-b516.fa | prodigal -d OceanDNA-b516/cds.fna -a OceanDNA-b516/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:50,475] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:50,476] [INFO] Task started: HMMsearch
[2023-03-18 21:15:50,476] [INFO] Running command: hmmsearch --tblout OceanDNA-b516/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/reference_markers.hmm OceanDNA-b516/protein.faa > /dev/null
[2023-03-18 21:15:50,709] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:50,710] [INFO] Found 6/6 markers.
[2023-03-18 21:15:50,738] [INFO] Query marker FASTA was written to OceanDNA-b516/markers.fasta
[2023-03-18 21:15:50,740] [INFO] Task started: Blastn
[2023-03-18 21:15:50,740] [INFO] Running command: blastn -query OceanDNA-b516/markers.fasta -db /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/reference_markers.fasta -out OceanDNA-b516/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:51,641] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:51,643] [INFO] Selected 24 target genomes.
[2023-03-18 21:15:51,644] [INFO] Target genome list was writen to OceanDNA-b516/target_genomes.txt
[2023-03-18 21:15:51,659] [INFO] Task started: fastANI
[2023-03-18 21:15:51,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg03cf10f8-a52d-4c36-acf4-a2b9ecf0d08f/OceanDNA-b516.fa --refList OceanDNA-b516/target_genomes.txt --output OceanDNA-b516/fastani_result.tsv --threads 1
[2023-03-18 21:16:11,272] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:11,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:16:11,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:16:11,286] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:16:11,286] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:16:11,286] [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	79.7541	516	1004	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.9206	380	1004	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.7689	269	1004	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.3193	326	1004	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3605	210	1004	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.1372	176	1004	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	75.9537	101	1004	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	75.1974	127	1004	95	below_threshold
Nocardioides terrae	strain=CGMCC 1.7056	GCA_900112345.1	574651	574651	type	True	75.1335	123	1004	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	75.1006	130	1004	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	75.0418	125	1004	95	below_threshold
Catellatospora methionotrophica	strain=NBRC 14553	GCA_016862655.1	121620	121620	type	True	75.0387	182	1004	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	75.0204	128	1004	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	75.0062	180	1004	95	below_threshold
Microlunatus sagamiharensis	strain=DSM 21743	GCA_900105785.1	546874	546874	type	True	74.9904	132	1004	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	74.9846	93	1004	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	74.9528	71	1004	95	below_threshold
Actinoplanes missouriensis	strain=431	GCA_000284295.1	1866	1866	type	True	74.9368	154	1004	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.9094	206	1004	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	74.9077	207	1004	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.9022	98	1004	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	74.9015	110	1004	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	74.6213	66	1004	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:16:11,287] [INFO] DFAST Taxonomy check result was written to OceanDNA-b516/tc_result.tsv
[2023-03-18 21:16:11,287] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:16:11,287] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:16:11,288] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/checkm_data
[2023-03-18 21:16:11,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:16:11,295] [INFO] Task started: CheckM
[2023-03-18 21:16:11,295] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b516/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b516/checkm_input OceanDNA-b516/checkm_result
[2023-03-18 21:17:16,695] [INFO] Task succeeded: CheckM
[2023-03-18 21:17:16,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.26%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:17:16,714] [INFO] ===== Completeness check finished =====
[2023-03-18 21:17:16,715] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:17:16,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b516/markers.fasta)
[2023-03-18 21:17:16,716] [INFO] Task started: Blastn
[2023-03-18 21:17:16,716] [INFO] Running command: blastn -query OceanDNA-b516/markers.fasta -db /var/lib/cwl/stg8b82e6c4-9fd3-4422-a9d9-4a8dd28dee80/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b516/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:17:18,310] [INFO] Task succeeded: Blastn
[2023-03-18 21:17:18,313] [INFO] Selected 21 target genomes.
[2023-03-18 21:17:18,313] [INFO] Target genome list was writen to OceanDNA-b516/target_genomes_gtdb.txt
[2023-03-18 21:17:18,336] [INFO] Task started: fastANI
[2023-03-18 21:17:18,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg03cf10f8-a52d-4c36-acf4-a2b9ecf0d08f/OceanDNA-b516.fa --refList OceanDNA-b516/target_genomes_gtdb.txt --output OceanDNA-b516/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:17:32,802] [INFO] Task succeeded: fastANI
[2023-03-18 21:17:32,814] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:17:32,814] [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_004364865.1	s__Ilumatobacter fluminis	79.7739	514	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	79.1269	402	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	78.239	289	1004	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_007693335.1	s__SKSP01 sp007693335	78.0934	298	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	78.0081	298	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.9351	379	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.7776	267	1004	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_009704985.1	s__VFMC01 sp009704985	77.4906	313	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	77.4592	231	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024485.1	s__Casp-actino5 sp010024485	77.4549	110	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCF_003426815.1	s__Desertimonas flava	77.3449	323	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013815505.1	s__JACDHN01 sp013815505	77.0345	146	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACDHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213665.1	s__UBA668 sp016213665	76.198	105	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	75.923	99	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155135.1	s__Bog-515 sp003155135	75.3665	78	1004	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCF_019039255.1	s__JABFXA01 sp019039255	75.19	128	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344865.1	s__Euzebya sp003344865	75.0973	131	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073135.1	s__Euzebya rosea	75.0556	129	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633575.1	s__Nocardioides sp003633575	75.0254	134	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	75.0112	130	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090295.1	s__Micromonospora coxensis	74.9314	147	1004	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:17:32,815] [INFO] GTDB search result was written to OceanDNA-b516/result_gtdb.tsv
[2023-03-18 21:17:32,816] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:17:32,820] [INFO] DFAST_QC result json was written to OceanDNA-b516/dqc_result.json
[2023-03-18 21:17:32,820] [INFO] DFAST_QC completed!
[2023-03-18 21:17:32,820] [INFO] Total running time: 0h2m3s