[2023-03-15 07:58:33,367] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,369] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference
[2023-03-15 07:58:35,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,137] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,137] [INFO] Running command: cat /var/lib/cwl/stg69247bff-cbcc-4bca-8972-d1f2f21ca477/OceanDNA-b35170.fa | prodigal -d OceanDNA-b35170/cds.fna -a OceanDNA-b35170/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:58:40,985] [INFO] Task succeeded: Prodigal
[2023-03-15 07:58:40,986] [INFO] Task started: HMMsearch
[2023-03-15 07:58:40,986] [INFO] Running command: hmmsearch --tblout OceanDNA-b35170/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/reference_markers.hmm OceanDNA-b35170/protein.faa > /dev/null
[2023-03-15 07:58:41,145] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:58:41,146] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg69247bff-cbcc-4bca-8972-d1f2f21ca477/OceanDNA-b35170.fa]
[2023-03-15 07:58:41,189] [INFO] Query marker FASTA was written to OceanDNA-b35170/markers.fasta
[2023-03-15 07:58:41,190] [INFO] Task started: Blastn
[2023-03-15 07:58:41,190] [INFO] Running command: blastn -query OceanDNA-b35170/markers.fasta -db /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/reference_markers.fasta -out OceanDNA-b35170/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:58:41,735] [INFO] Task succeeded: Blastn
[2023-03-15 07:58:41,741] [INFO] Selected 16 target genomes.
[2023-03-15 07:58:41,741] [INFO] Target genome list was writen to OceanDNA-b35170/target_genomes.txt
[2023-03-15 07:58:41,751] [INFO] Task started: fastANI
[2023-03-15 07:58:41,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg69247bff-cbcc-4bca-8972-d1f2f21ca477/OceanDNA-b35170.fa --refList OceanDNA-b35170/target_genomes.txt --output OceanDNA-b35170/fastani_result.tsv --threads 1
[2023-03-15 07:58:49,703] [INFO] Task succeeded: fastANI
[2023-03-15 07:58:49,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:58:49,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:58:49,709] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:58:49,709] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:58:49,709] [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	94.8764	247	262	95	below_threshold
Kangiella taiwanensis	strain=KT1	GCA_020005165.1	1079179	1079179	type	True	81.7201	185	262	95	below_threshold
Kangiella spongicola	strain=ATCC BAA-2076	GCA_003194565.2	796379	796379	type	True	79.2936	130	262	95	below_threshold
Kangiella sediminilitoris	strain=KCTC 23892	GCA_001708405.1	1144748	1144748	type	True	78.975	92	262	95	below_threshold
Kangiella shandongensis	strain=PI	GCA_020005365.1	2763258	2763258	type	True	78.8776	114	262	95	below_threshold
Kangiella koreensis	strain=DSM 16069	GCA_000024085.1	261964	261964	type	True	77.708	57	262	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:58:49,712] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35170/tc_result.tsv
[2023-03-15 07:58:49,715] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:58:49,715] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:58:49,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/checkm_data
[2023-03-15 07:58:49,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:58:49,722] [INFO] Task started: CheckM
[2023-03-15 07:58:49,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35170/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35170/checkm_input OceanDNA-b35170/checkm_result
[2023-03-15 07:59:10,355] [INFO] Task succeeded: CheckM
[2023-03-15 07:59:10,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.58%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:59:10,565] [INFO] ===== Completeness check finished =====
[2023-03-15 07:59:10,565] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:59:10,565] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35170/markers.fasta)
[2023-03-15 07:59:10,566] [INFO] Task started: Blastn
[2023-03-15 07:59:10,566] [INFO] Running command: blastn -query OceanDNA-b35170/markers.fasta -db /var/lib/cwl/stgc11506be-135f-449f-b240-6a7d6123fb38/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35170/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:11,339] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:11,368] [INFO] Selected 13 target genomes.
[2023-03-15 07:59:11,368] [INFO] Target genome list was writen to OceanDNA-b35170/target_genomes_gtdb.txt
[2023-03-15 07:59:11,397] [INFO] Task started: fastANI
[2023-03-15 07:59:11,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg69247bff-cbcc-4bca-8972-d1f2f21ca477/OceanDNA-b35170.fa --refList OceanDNA-b35170/target_genomes_gtdb.txt --output OceanDNA-b35170/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:59:16,937] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:16,942] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:59:16,942] [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	94.8764	247	262	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	81.1562	98	262	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	79.2936	130	262	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	78.975	92	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024085.1	s__Kangiella koreensis	77.708	57	262	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	77.4741	50	262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Kangiellaceae;g__Kangiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:59:16,945] [INFO] GTDB search result was written to OceanDNA-b35170/result_gtdb.tsv
[2023-03-15 07:59:16,948] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:59:16,952] [INFO] DFAST_QC result json was written to OceanDNA-b35170/dqc_result.json
[2023-03-15 07:59:16,952] [INFO] DFAST_QC completed!
[2023-03-15 07:59:16,952] [INFO] Total running time: 0h0m44s