[2023-03-19 00:33:18,976] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:18,976] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:18,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference
[2023-03-19 00:33:20,169] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,169] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,169] [INFO] Running command: cat /var/lib/cwl/stg1652a8de-93c1-422e-933b-ed9516204234/OceanDNA-b7210.fa | prodigal -d OceanDNA-b7210/cds.fna -a OceanDNA-b7210/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:25,179] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:25,179] [INFO] Task started: HMMsearch
[2023-03-19 00:33:25,180] [INFO] Running command: hmmsearch --tblout OceanDNA-b7210/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/reference_markers.hmm OceanDNA-b7210/protein.faa > /dev/null
[2023-03-19 00:33:25,337] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:25,338] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1652a8de-93c1-422e-933b-ed9516204234/OceanDNA-b7210.fa]
[2023-03-19 00:33:25,356] [INFO] Query marker FASTA was written to OceanDNA-b7210/markers.fasta
[2023-03-19 00:33:25,358] [INFO] Task started: Blastn
[2023-03-19 00:33:25,358] [INFO] Running command: blastn -query OceanDNA-b7210/markers.fasta -db /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/reference_markers.fasta -out OceanDNA-b7210/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:25,867] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:25,869] [INFO] Selected 14 target genomes.
[2023-03-19 00:33:25,869] [INFO] Target genome list was writen to OceanDNA-b7210/target_genomes.txt
[2023-03-19 00:33:25,883] [INFO] Task started: fastANI
[2023-03-19 00:33:25,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg1652a8de-93c1-422e-933b-ed9516204234/OceanDNA-b7210.fa --refList OceanDNA-b7210/target_genomes.txt --output OceanDNA-b7210/fastani_result.tsv --threads 1
[2023-03-19 00:33:33,309] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:33,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:33,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:33,314] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:33,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:33:33,314] [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
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	86.9403	83	97	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	80.8707	54	97	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	80.7728	51	97	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	80.4231	58	97	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	80.4231	58	97	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:33:33,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7210/tc_result.tsv
[2023-03-19 00:33:33,315] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:33,315] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:33,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/checkm_data
[2023-03-19 00:33:33,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:33,319] [INFO] Task started: CheckM
[2023-03-19 00:33:33,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7210/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7210/checkm_input OceanDNA-b7210/checkm_result
[2023-03-19 00:33:53,689] [INFO] Task succeeded: CheckM
[2023-03-19 00:33:53,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:33:53,691] [INFO] ===== Completeness check finished =====
[2023-03-19 00:33:53,691] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:33:53,691] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7210/markers.fasta)
[2023-03-19 00:33:53,692] [INFO] Task started: Blastn
[2023-03-19 00:33:53,693] [INFO] Running command: blastn -query OceanDNA-b7210/markers.fasta -db /var/lib/cwl/stg341ecb26-7f46-4fc4-90cb-442d008c9fdf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7210/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:54,397] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:54,398] [INFO] Selected 12 target genomes.
[2023-03-19 00:33:54,398] [INFO] Target genome list was writen to OceanDNA-b7210/target_genomes_gtdb.txt
[2023-03-19 00:33:54,470] [INFO] Task started: fastANI
[2023-03-19 00:33:54,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg1652a8de-93c1-422e-933b-ed9516204234/OceanDNA-b7210.fa --refList OceanDNA-b7210/target_genomes_gtdb.txt --output OceanDNA-b7210/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:01,631] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:01,636] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:34:01,636] [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_006714895.1	s__Gramella sp006714895	96.171	89	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423045.1	s__Gramella portivictoriae	86.9403	83	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	80.797	55	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_003054225.1	s__Gramella gaetbulicola	80.7728	51	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	80.4231	58	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105135.1	s__Gramella sp900105135	79.3395	50	97	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:01,637] [INFO] GTDB search result was written to OceanDNA-b7210/result_gtdb.tsv
[2023-03-19 00:34:01,637] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:01,638] [INFO] DFAST_QC result json was written to OceanDNA-b7210/dqc_result.json
[2023-03-19 00:34:01,639] [INFO] DFAST_QC completed!
[2023-03-19 00:34:01,639] [INFO] Total running time: 0h0m43s