[2023-03-19 04:43:18,646] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,646] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference
[2023-03-19 04:43:19,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,743] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,743] [INFO] Running command: cat /var/lib/cwl/stgc16489de-49f9-48e7-89ba-51e8dc70ecfd/OceanDNA-b3673.fa | prodigal -d OceanDNA-b3673/cds.fna -a OceanDNA-b3673/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:38,873] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:38,873] [INFO] Task started: HMMsearch
[2023-03-19 04:43:38,873] [INFO] Running command: hmmsearch --tblout OceanDNA-b3673/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/reference_markers.hmm OceanDNA-b3673/protein.faa > /dev/null
[2023-03-19 04:43:39,052] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:39,052] [INFO] Found 6/6 markers.
[2023-03-19 04:43:39,071] [INFO] Query marker FASTA was written to OceanDNA-b3673/markers.fasta
[2023-03-19 04:43:39,072] [INFO] Task started: Blastn
[2023-03-19 04:43:39,072] [INFO] Running command: blastn -query OceanDNA-b3673/markers.fasta -db /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/reference_markers.fasta -out OceanDNA-b3673/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:39,662] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:39,662] [INFO] Selected 28 target genomes.
[2023-03-19 04:43:39,663] [INFO] Target genome list was writen to OceanDNA-b3673/target_genomes.txt
[2023-03-19 04:43:39,678] [INFO] Task started: fastANI
[2023-03-19 04:43:39,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgc16489de-49f9-48e7-89ba-51e8dc70ecfd/OceanDNA-b3673.fa --refList OceanDNA-b3673/target_genomes.txt --output OceanDNA-b3673/fastani_result.tsv --threads 1
[2023-03-19 04:43:58,424] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:58,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:58,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:58,434] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:58,434] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:43:58,434] [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
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	75.934	81	810	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	75.8982	83	810	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	75.5315	53	810	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	75.3469	56	810	95	below_threshold
Hymenobacter coccineus	strain=CCM 8649	GCA_001816125.1	1908235	1908235	type	True	75.1209	63	810	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	74.8877	76	810	95	below_threshold
Tessaracoccus oleiagri	strain=CGMCC 1.9159	GCA_900103275.1	686624	686624	type	True	74.8785	76	810	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	74.8155	54	810	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	74.7912	126	810	95	below_threshold
Gryllotalpicola ginsengisoli	strain=DSM 22003	GCA_000419445.1	444608	444608	type	True	74.7883	93	810	95	below_threshold
Methylobacterium indicum	strain=SE2.11	GCA_001043895.1	1775910	1775910	type	True	74.785	127	810	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	74.7762	120	810	95	below_threshold
Microbacterium resistens	strain=NBRC 103078	GCA_001552355.1	156977	156977	type	True	74.7205	85	810	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	74.7038	149	810	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	74.701	178	810	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	74.635	153	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:43:58,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3673/tc_result.tsv
[2023-03-19 04:43:58,435] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:58,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:58,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/checkm_data
[2023-03-19 04:43:58,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:58,476] [INFO] Task started: CheckM
[2023-03-19 04:43:58,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3673/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3673/checkm_input OceanDNA-b3673/checkm_result
[2023-03-19 04:44:45,788] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:45,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:45,791] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:45,791] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:45,792] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3673/markers.fasta)
[2023-03-19 04:44:45,792] [INFO] Task started: Blastn
[2023-03-19 04:44:45,792] [INFO] Running command: blastn -query OceanDNA-b3673/markers.fasta -db /var/lib/cwl/stg5202cdd9-d4e6-411e-96e5-e139afe2c678/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3673/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:46,714] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:46,715] [INFO] Selected 28 target genomes.
[2023-03-19 04:44:46,715] [INFO] Target genome list was writen to OceanDNA-b3673/target_genomes_gtdb.txt
[2023-03-19 04:44:46,893] [INFO] Task started: fastANI
[2023-03-19 04:44:46,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgc16489de-49f9-48e7-89ba-51e8dc70ecfd/OceanDNA-b3673.fa --refList OceanDNA-b3673/target_genomes_gtdb.txt --output OceanDNA-b3673/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:45:04,701] [INFO] Task succeeded: fastANI
[2023-03-19 04:45:04,710] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:45:04,710] [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_015490175.1	s__WFYJ01 sp015490175	76.0797	70	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__WFYJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	76.0439	76	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	75.8808	84	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803465.1	s__Lewinella_A litorea	75.3469	56	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001816125.1	s__Hymenobacter coccineus	75.1131	64	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439025.1	s__Hymenobacter nivis_A	75.0595	72	810	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002929555.1	s__Cryobacterium sp002929555	74.8522	50	810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702655.1	s__CAIKUF01 sp016702655	74.8439	117	810	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	74.8434	139	810	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847545.1	s__CAINDZ01 sp903847545	74.8139	54	810	d__Bacteria;p__Krumholzibacteriota;c__Krumholzibacteria;o__LZORAL124-64-63;f__LZORAL124-64-63;g__CAINDZ01	95.0	98.70	98.54	0.79	0.77	4	-
GCA_006226565.1	s__PHBI01 sp006226565	74.7954	222	810	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	74.7098	146	810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916505.1	s__Naasia sp017916505	74.7084	105	810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Naasia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	74.6465	118	810	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:45:04,710] [INFO] GTDB search result was written to OceanDNA-b3673/result_gtdb.tsv
[2023-03-19 04:45:04,710] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:45:04,712] [INFO] DFAST_QC result json was written to OceanDNA-b3673/dqc_result.json
[2023-03-19 04:45:04,712] [INFO] DFAST_QC completed!
[2023-03-19 04:45:04,712] [INFO] Total running time: 0h1m46s