[2023-03-19 00:19:08,845] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:19:08,845] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:19:08,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference
[2023-03-19 00:19:10,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:19:10,386] [INFO] Task started: Prodigal
[2023-03-19 00:19:10,387] [INFO] Running command: cat /var/lib/cwl/stgd6b03593-2787-4f8c-b89f-721794943ff8/OceanDNA-b35174.fa | prodigal -d OceanDNA-b35174/cds.fna -a OceanDNA-b35174/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:19:22,519] [INFO] Task succeeded: Prodigal
[2023-03-19 00:19:22,519] [INFO] Task started: HMMsearch
[2023-03-19 00:19:22,519] [INFO] Running command: hmmsearch --tblout OceanDNA-b35174/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/reference_markers.hmm OceanDNA-b35174/protein.faa > /dev/null
[2023-03-19 00:19:22,713] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:19:22,714] [INFO] Found 6/6 markers.
[2023-03-19 00:19:22,730] [INFO] Query marker FASTA was written to OceanDNA-b35174/markers.fasta
[2023-03-19 00:19:22,731] [INFO] Task started: Blastn
[2023-03-19 00:19:22,731] [INFO] Running command: blastn -query OceanDNA-b35174/markers.fasta -db /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/reference_markers.fasta -out OceanDNA-b35174/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:19:23,314] [INFO] Task succeeded: Blastn
[2023-03-19 00:19:23,315] [INFO] Selected 17 target genomes.
[2023-03-19 00:19:23,315] [INFO] Target genome list was writen to OceanDNA-b35174/target_genomes.txt
[2023-03-19 00:19:23,325] [INFO] Task started: fastANI
[2023-03-19 00:19:23,325] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b03593-2787-4f8c-b89f-721794943ff8/OceanDNA-b35174.fa --refList OceanDNA-b35174/target_genomes.txt --output OceanDNA-b35174/fastani_result.tsv --threads 1
[2023-03-19 00:19:31,883] [INFO] Task succeeded: fastANI
[2023-03-19 00:19:31,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:19:31,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:19:31,890] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:19:31,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:19:31,890] [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
Kangiella geojedonensis	strain=YCS-5	GCA_000981765.1	914150	914150	type	True	86.7115	622	736	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	81.541	475	736	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	79.616	342	736	95	below_threshold
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	79.2458	221	736	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	78.9559	268	736	95	below_threshold
Kangiella profundi	strain=FT102	GCA_002838765.1	1561924	1561924	type	True	77.6488	116	736	95	below_threshold
Kangiella profundi	strain=CGMCC 1.12959	GCA_014640235.1	1561924	1561924	type	True	77.6332	114	736	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:19:31,891] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35174/tc_result.tsv
[2023-03-19 00:19:31,891] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:19:31,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:19:31,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/checkm_data
[2023-03-19 00:19:31,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:19:31,895] [INFO] Task started: CheckM
[2023-03-19 00:19:31,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35174/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35174/checkm_input OceanDNA-b35174/checkm_result
[2023-03-19 00:20:06,160] [INFO] Task succeeded: CheckM
[2023-03-19 00:20:06,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.63%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-19 00:20:06,165] [INFO] ===== Completeness check finished =====
[2023-03-19 00:20:06,165] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:20:06,165] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35174/markers.fasta)
[2023-03-19 00:20:06,167] [INFO] Task started: Blastn
[2023-03-19 00:20:06,167] [INFO] Running command: blastn -query OceanDNA-b35174/markers.fasta -db /var/lib/cwl/stg625ee9a9-e7ec-448b-afd8-cbb60538119d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35174/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:20:06,967] [INFO] Task succeeded: Blastn
[2023-03-19 00:20:06,968] [INFO] Selected 18 target genomes.
[2023-03-19 00:20:06,968] [INFO] Target genome list was writen to OceanDNA-b35174/target_genomes_gtdb.txt
[2023-03-19 00:20:06,986] [INFO] Task started: fastANI
[2023-03-19 00:20:06,986] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6b03593-2787-4f8c-b89f-721794943ff8/OceanDNA-b35174.fa --refList OceanDNA-b35174/target_genomes_gtdb.txt --output OceanDNA-b35174/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:20:14,553] [INFO] Task succeeded: fastANI
[2023-03-19 00:20:14,559] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:20:14,559] [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_000981765.1	s__Kangiella geojedonensis	86.7115	622	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003370465.1	s__Kangiella sp003370465	81.6337	262	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003194565.2	s__Kangiella spongicola	79.616	342	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	96.32	96.32	0.92	0.92	2	-
GCF_001708405.1	s__Kangiella sediminilitoris	79.2458	221	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762745.1	s__Kangiella sp014762745	77.6786	112	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002838765.1	s__Kangiella profundi	77.6488	116	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000024085.1	s__Kangiella koreensis	77.6055	129	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374105.1	s__Kangiella aquimarina	77.5345	126	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373015.1	s__Kangiella sp013373015	76.9801	102	736	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:20:14,560] [INFO] GTDB search result was written to OceanDNA-b35174/result_gtdb.tsv
[2023-03-19 00:20:14,560] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:20:14,561] [INFO] DFAST_QC result json was written to OceanDNA-b35174/dqc_result.json
[2023-03-19 00:20:14,561] [INFO] DFAST_QC completed!
[2023-03-19 00:20:14,561] [INFO] Total running time: 0h1m6s