[2023-03-17 08:11:32,979] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,979] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference
[2023-03-17 08:11:34,670] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:34,670] [INFO] Task started: Prodigal
[2023-03-17 08:11:34,671] [INFO] Running command: cat /var/lib/cwl/stge5ff62bc-de56-4dac-beda-1a6306db208a/OceanDNA-b9652.fa | prodigal -d OceanDNA-b9652/cds.fna -a OceanDNA-b9652/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:58,745] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:58,745] [INFO] Task started: HMMsearch
[2023-03-17 08:11:58,745] [INFO] Running command: hmmsearch --tblout OceanDNA-b9652/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/reference_markers.hmm OceanDNA-b9652/protein.faa > /dev/null
[2023-03-17 08:11:58,949] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:58,950] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge5ff62bc-de56-4dac-beda-1a6306db208a/OceanDNA-b9652.fa]
[2023-03-17 08:11:58,971] [INFO] Query marker FASTA was written to OceanDNA-b9652/markers.fasta
[2023-03-17 08:11:58,972] [INFO] Task started: Blastn
[2023-03-17 08:11:58,972] [INFO] Running command: blastn -query OceanDNA-b9652/markers.fasta -db /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/reference_markers.fasta -out OceanDNA-b9652/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:59,538] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:59,539] [INFO] Selected 14 target genomes.
[2023-03-17 08:11:59,539] [INFO] Target genome list was writen to OceanDNA-b9652/target_genomes.txt
[2023-03-17 08:11:59,573] [INFO] Task started: fastANI
[2023-03-17 08:11:59,573] [INFO] Running command: fastANI --query /var/lib/cwl/stge5ff62bc-de56-4dac-beda-1a6306db208a/OceanDNA-b9652.fa --refList OceanDNA-b9652/target_genomes.txt --output OceanDNA-b9652/fastani_result.tsv --threads 1
[2023-03-17 08:12:10,060] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:10,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:12:10,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:12:10,069] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:12:10,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:12:10,069] [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
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	85.5901	838	1239	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	84.6857	827	1239	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	81.3123	762	1239	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.8427	724	1239	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	80.5451	689	1239	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	80.4758	675	1239	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.4078	708	1239	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	79.7122	611	1239	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.5849	74	1239	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	75.9925	81	1239	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	75.9534	81	1239	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	75.635	80	1239	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:12:10,069] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9652/tc_result.tsv
[2023-03-17 08:12:10,069] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:12:10,070] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:12:10,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/checkm_data
[2023-03-17 08:12:10,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:12:10,075] [INFO] Task started: CheckM
[2023-03-17 08:12:10,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9652/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9652/checkm_input OceanDNA-b9652/checkm_result
[2023-03-17 08:13:09,517] [INFO] Task succeeded: CheckM
[2023-03-17 08:13:09,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:13:09,520] [INFO] ===== Completeness check finished =====
[2023-03-17 08:13:09,520] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:13:09,521] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9652/markers.fasta)
[2023-03-17 08:13:09,522] [INFO] Task started: Blastn
[2023-03-17 08:13:09,522] [INFO] Running command: blastn -query OceanDNA-b9652/markers.fasta -db /var/lib/cwl/stg4c5ec7a5-9660-4408-a6bc-2324fe7314b4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9652/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:13:10,308] [INFO] Task succeeded: Blastn
[2023-03-17 08:13:10,309] [INFO] Selected 10 target genomes.
[2023-03-17 08:13:10,309] [INFO] Target genome list was writen to OceanDNA-b9652/target_genomes_gtdb.txt
[2023-03-17 08:13:10,367] [INFO] Task started: fastANI
[2023-03-17 08:13:10,367] [INFO] Running command: fastANI --query /var/lib/cwl/stge5ff62bc-de56-4dac-beda-1a6306db208a/OceanDNA-b9652.fa --refList OceanDNA-b9652/target_genomes_gtdb.txt --output OceanDNA-b9652/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:13:19,488] [INFO] Task succeeded: fastANI
[2023-03-17 08:13:19,496] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:13:19,496] [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_900167935.1	s__Maribacter arcticus	85.582	839	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	84.7056	825	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	82.0981	783	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900112245.1	s__Maribacter stanieri	81.3156	762	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.8394	724	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771495.1	s__Maribacter sp005771495	80.795	700	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	80.4691	675	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.4126	707	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900155985.1	s__Maribacter ulvicola	79.7167	610	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	75.635	80	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-17 08:13:19,496] [INFO] GTDB search result was written to OceanDNA-b9652/result_gtdb.tsv
[2023-03-17 08:13:19,496] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:13:19,497] [INFO] DFAST_QC result json was written to OceanDNA-b9652/dqc_result.json
[2023-03-17 08:13:19,498] [INFO] DFAST_QC completed!
[2023-03-17 08:13:19,498] [INFO] Total running time: 0h1m47s