[2023-03-15 12:33:51,630] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:33:51,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:33:51,630] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference
[2023-03-15 12:33:52,742] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:33:52,743] [INFO] Task started: Prodigal
[2023-03-15 12:33:52,743] [INFO] Running command: cat /var/lib/cwl/stg33bfd4f0-4bb0-4741-aad1-23a33bf2ee0d/OceanDNA-b3887.fa | prodigal -d OceanDNA-b3887/cds.fna -a OceanDNA-b3887/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:34:26,894] [INFO] Task succeeded: Prodigal
[2023-03-15 12:34:26,895] [INFO] Task started: HMMsearch
[2023-03-15 12:34:26,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b3887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/reference_markers.hmm OceanDNA-b3887/protein.faa > /dev/null
[2023-03-15 12:34:27,150] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:34:27,150] [INFO] Found 6/6 markers.
[2023-03-15 12:34:27,198] [INFO] Query marker FASTA was written to OceanDNA-b3887/markers.fasta
[2023-03-15 12:34:27,199] [INFO] Task started: Blastn
[2023-03-15 12:34:27,199] [INFO] Running command: blastn -query OceanDNA-b3887/markers.fasta -db /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/reference_markers.fasta -out OceanDNA-b3887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:34:27,753] [INFO] Task succeeded: Blastn
[2023-03-15 12:34:27,754] [INFO] Selected 29 target genomes.
[2023-03-15 12:34:27,755] [INFO] Target genome list was writen to OceanDNA-b3887/target_genomes.txt
[2023-03-15 12:34:27,806] [INFO] Task started: fastANI
[2023-03-15 12:34:27,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg33bfd4f0-4bb0-4741-aad1-23a33bf2ee0d/OceanDNA-b3887.fa --refList OceanDNA-b3887/target_genomes.txt --output OceanDNA-b3887/fastani_result.tsv --threads 1
[2023-03-15 12:34:47,944] [INFO] Task succeeded: fastANI
[2023-03-15 12:34:47,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:34:47,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:34:47,954] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:34:47,954] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:34:47,954] [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
Bernardetia litoralis	strain=DSM 6794	GCA_000265505.1	999	999	type	True	84.2731	1242	1778	95	below_threshold
Flammeovirga kamogawensis	strain=YS10	GCA_007097495.1	373891	373891	type	True	75.1919	67	1778	95	below_threshold
Flammeovirga kamogawensis	strain=DSM 26273	GCA_014207545.1	373891	373891	type	True	75.18	68	1778	95	below_threshold
Flammeovirga kamogawensis	strain=YS10	GCA_018736065.1	373891	373891	type	True	75.1796	68	1778	95	below_threshold
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	75.0874	76	1778	95	below_threshold
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	75.0744	64	1778	95	below_threshold
Flammeovirga pectinis	strain=L12M1	GCA_003970675.1	2494373	2494373	type	True	74.9727	77	1778	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	74.8277	65	1778	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	74.8039	61	1778	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	74.7671	80	1778	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	74.7648	54	1778	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	74.7192	61	1778	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	74.6858	62	1778	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	74.6858	62	1778	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:34:47,956] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3887/tc_result.tsv
[2023-03-15 12:34:47,957] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:34:47,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:34:47,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/checkm_data
[2023-03-15 12:34:47,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:34:47,967] [INFO] Task started: CheckM
[2023-03-15 12:34:47,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3887/checkm_input OceanDNA-b3887/checkm_result
[2023-03-15 12:36:11,457] [INFO] Task succeeded: CheckM
[2023-03-15 12:36:11,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:36:11,513] [INFO] ===== Completeness check finished =====
[2023-03-15 12:36:11,514] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:36:11,514] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3887/markers.fasta)
[2023-03-15 12:36:11,515] [INFO] Task started: Blastn
[2023-03-15 12:36:11,515] [INFO] Running command: blastn -query OceanDNA-b3887/markers.fasta -db /var/lib/cwl/stgb6b48576-15eb-4e0a-96da-b8f3037649fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:36:12,241] [INFO] Task succeeded: Blastn
[2023-03-15 12:36:12,248] [INFO] Selected 23 target genomes.
[2023-03-15 12:36:12,248] [INFO] Target genome list was writen to OceanDNA-b3887/target_genomes_gtdb.txt
[2023-03-15 12:36:12,877] [INFO] Task started: fastANI
[2023-03-15 12:36:12,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg33bfd4f0-4bb0-4741-aad1-23a33bf2ee0d/OceanDNA-b3887.fa --refList OceanDNA-b3887/target_genomes_gtdb.txt --output OceanDNA-b3887/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:36:30,787] [INFO] Task succeeded: fastANI
[2023-03-15 12:36:30,795] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:36:30,795] [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_002784125.1	s__Bernardetia sp002784125	87.2229	1000	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Bernardetiaceae;g__Bernardetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265505.1	s__Bernardetia litoralis	84.2978	1238	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Bernardetiaceae;g__Bernardetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018736065.1	s__Flammeovirga kamogawensis	75.1704	69	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003148625.1	s__Arcicella aurantiaca	75.1053	74	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644295.1	s__Emticicia aquatilis	75.0744	64	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298865.1	s__JAAFJL01 sp013298865	75.0018	55	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970675.1	s__Flammeovirga pectinis	74.9727	77	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495105.1	s__Emticicia sp017495105	74.925	58	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707955.1	s__Flavobacterium sp009707955	74.8471	76	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012524075.1	s__Lutibacter sp012524075	74.8075	51	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967805.1	s__Flavobacterium sp000967805	74.7941	75	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015767265.1	s__Aureivirga marina	74.771	79	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	74.6865	61	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014784055.1	s__Polaribacter haliotis	74.6858	62	1778	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:36:30,798] [INFO] GTDB search result was written to OceanDNA-b3887/result_gtdb.tsv
[2023-03-15 12:36:30,798] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:36:30,802] [INFO] DFAST_QC result json was written to OceanDNA-b3887/dqc_result.json
[2023-03-15 12:36:30,802] [INFO] DFAST_QC completed!
[2023-03-15 12:36:30,802] [INFO] Total running time: 0h2m39s