[2023-03-16 03:23:49,840] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:49,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:49,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference
[2023-03-16 03:23:50,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,974] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,975] [INFO] Running command: cat /var/lib/cwl/stgc6d79a63-da70-42cc-a3af-7506389db7bd/OceanDNA-b6509.fa | prodigal -d OceanDNA-b6509/cds.fna -a OceanDNA-b6509/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:19,186] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:19,186] [INFO] Task started: HMMsearch
[2023-03-16 03:24:19,186] [INFO] Running command: hmmsearch --tblout OceanDNA-b6509/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/reference_markers.hmm OceanDNA-b6509/protein.faa > /dev/null
[2023-03-16 03:24:19,410] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:19,410] [INFO] Found 6/6 markers.
[2023-03-16 03:24:19,435] [INFO] Query marker FASTA was written to OceanDNA-b6509/markers.fasta
[2023-03-16 03:24:19,435] [INFO] Task started: Blastn
[2023-03-16 03:24:19,435] [INFO] Running command: blastn -query OceanDNA-b6509/markers.fasta -db /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/reference_markers.fasta -out OceanDNA-b6509/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:20,036] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:20,037] [INFO] Selected 19 target genomes.
[2023-03-16 03:24:20,038] [INFO] Target genome list was writen to OceanDNA-b6509/target_genomes.txt
[2023-03-16 03:24:20,047] [INFO] Task started: fastANI
[2023-03-16 03:24:20,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d79a63-da70-42cc-a3af-7506389db7bd/OceanDNA-b6509.fa --refList OceanDNA-b6509/target_genomes.txt --output OceanDNA-b6509/fastani_result.tsv --threads 1
[2023-03-16 03:24:35,703] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:35,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:35,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:35,713] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:35,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:35,714] [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
Arenibacter aquaticus	strain=GUO	GCA_003957295.1	2489054	2489054	type	True	91.0922	1108	1258	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	79.0847	575	1258	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	79.0193	565	1258	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	79.0134	579	1258	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	78.9099	565	1258	95	below_threshold
Arenibacter hampyeongensis	strain=JCM 17788	GCA_002909255.1	1028743	1028743	type	True	78.6917	534	1258	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	78.6893	543	1258	95	below_threshold
Arenibacter catalasegens	strain=P308H10	GCA_002909235.1	2056779	2056779	type	True	78.4982	499	1258	95	below_threshold
Arenibacter certesii	strain=KCTC 12113	GCA_014651295.1	228955	228955	type	True	77.23	238	1258	95	below_threshold
Arenibacter certesii	strain=DSM 19833	GCA_000429545.1	228955	228955	type	True	77.2154	240	1258	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	76.64	203	1258	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.4742	108	1258	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	75.9772	68	1258	95	below_threshold
Maribacter arenosus	strain=CAU 1321	GCA_014610845.1	1854708	1854708	type	True	75.9366	94	1258	95	below_threshold
Kriegella aquimaris	strain=DSM 19886	GCA_900103215.1	192904	192904	type	True	75.8267	109	1258	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	75.3423	52	1258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:35,714] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6509/tc_result.tsv
[2023-03-16 03:24:35,714] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:35,714] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:35,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/checkm_data
[2023-03-16 03:24:35,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:35,720] [INFO] Task started: CheckM
[2023-03-16 03:24:35,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6509/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6509/checkm_input OceanDNA-b6509/checkm_result
[2023-03-16 03:25:44,013] [INFO] Task succeeded: CheckM
[2023-03-16 03:25:44,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:25:44,016] [INFO] ===== Completeness check finished =====
[2023-03-16 03:25:44,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:25:44,016] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6509/markers.fasta)
[2023-03-16 03:25:44,016] [INFO] Task started: Blastn
[2023-03-16 03:25:44,017] [INFO] Running command: blastn -query OceanDNA-b6509/markers.fasta -db /var/lib/cwl/stg80e9ae91-7cc0-440e-a12e-44e289ceece2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6509/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:25:45,057] [INFO] Task succeeded: Blastn
[2023-03-16 03:25:45,058] [INFO] Selected 12 target genomes.
[2023-03-16 03:25:45,058] [INFO] Target genome list was writen to OceanDNA-b6509/target_genomes_gtdb.txt
[2023-03-16 03:25:45,129] [INFO] Task started: fastANI
[2023-03-16 03:25:45,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d79a63-da70-42cc-a3af-7506389db7bd/OceanDNA-b6509.fa --refList OceanDNA-b6509/target_genomes_gtdb.txt --output OceanDNA-b6509/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:57,063] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:57,071] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:25:57,071] [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_003957295.1	s__Arenibacter aquaticus	91.0922	1108	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	79.0906	574	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_014397245.1	s__Arenibacter arenosicollis	79.0465	561	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	79.009	579	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
GCF_900177645.1	s__Arenibacter troitsensis	78.8986	567	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	78.816	603	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909255.1	s__Arenibacter hampyeongensis	78.6922	533	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259375.1	s__Arenibacter echinorum	78.6852	543	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	78.6517	523	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426735.1	s__Arenibacter sp003426735	78.496	482	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002909235.1	s__Arenibacter catalasegens	78.4951	498	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429545.1	s__Arenibacter certesii	77.2154	240	1258	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:57,071] [INFO] GTDB search result was written to OceanDNA-b6509/result_gtdb.tsv
[2023-03-16 03:25:57,071] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:57,073] [INFO] DFAST_QC result json was written to OceanDNA-b6509/dqc_result.json
[2023-03-16 03:25:57,073] [INFO] DFAST_QC completed!
[2023-03-16 03:25:57,073] [INFO] Total running time: 0h2m7s