[2023-03-18 22:16:20,354] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:16:20,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:16:20,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference
[2023-03-18 22:16:21,480] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:16:21,480] [INFO] Task started: Prodigal
[2023-03-18 22:16:21,481] [INFO] Running command: cat /var/lib/cwl/stg31834626-f975-4516-b63d-8e9a1c520555/OceanDNA-b9687.fa | prodigal -d OceanDNA-b9687/cds.fna -a OceanDNA-b9687/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:16:42,255] [INFO] Task succeeded: Prodigal
[2023-03-18 22:16:42,255] [INFO] Task started: HMMsearch
[2023-03-18 22:16:42,255] [INFO] Running command: hmmsearch --tblout OceanDNA-b9687/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/reference_markers.hmm OceanDNA-b9687/protein.faa > /dev/null
[2023-03-18 22:16:42,470] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:16:42,470] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg31834626-f975-4516-b63d-8e9a1c520555/OceanDNA-b9687.fa]
[2023-03-18 22:16:42,496] [INFO] Query marker FASTA was written to OceanDNA-b9687/markers.fasta
[2023-03-18 22:16:42,497] [INFO] Task started: Blastn
[2023-03-18 22:16:42,497] [INFO] Running command: blastn -query OceanDNA-b9687/markers.fasta -db /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/reference_markers.fasta -out OceanDNA-b9687/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:16:43,116] [INFO] Task succeeded: Blastn
[2023-03-18 22:16:43,117] [INFO] Selected 14 target genomes.
[2023-03-18 22:16:43,117] [INFO] Target genome list was writen to OceanDNA-b9687/target_genomes.txt
[2023-03-18 22:16:43,124] [INFO] Task started: fastANI
[2023-03-18 22:16:43,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg31834626-f975-4516-b63d-8e9a1c520555/OceanDNA-b9687.fa --refList OceanDNA-b9687/target_genomes.txt --output OceanDNA-b9687/fastani_result.tsv --threads 1
[2023-03-18 22:16:53,467] [INFO] Task succeeded: fastANI
[2023-03-18 22:16:53,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:16:53,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:16:53,474] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 22:16:53,474] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 22:16:53,474] [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 litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	97.4208	881	959	95	conclusive
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	84.2716	792	959	95	below_threshold
Maribacter forsetii	strain=DSM 18668	GCA_000744105.1	444515	444515	type	True	83.7416	710	959	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	83.4886	647	959	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	81.5137	628	959	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	81.4231	631	959	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	81.4202	629	959	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	81.045	648	959	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	79.1792	393	959	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.6139	64	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:16:53,475] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9687/tc_result.tsv
[2023-03-18 22:16:53,475] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:16:53,475] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:16:53,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/checkm_data
[2023-03-18 22:16:53,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:16:53,481] [INFO] Task started: CheckM
[2023-03-18 22:16:53,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9687/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9687/checkm_input OceanDNA-b9687/checkm_result
[2023-03-18 22:17:46,965] [INFO] Task succeeded: CheckM
[2023-03-18 22:17:46,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.57%
Contamintation: 5.09%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:17:46,968] [INFO] ===== Completeness check finished =====
[2023-03-18 22:17:46,968] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:17:46,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9687/markers.fasta)
[2023-03-18 22:17:46,969] [INFO] Task started: Blastn
[2023-03-18 22:17:46,969] [INFO] Running command: blastn -query OceanDNA-b9687/markers.fasta -db /var/lib/cwl/stg3b086277-14bf-4ddb-8708-df78c10e68ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9687/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:17:47,919] [INFO] Task succeeded: Blastn
[2023-03-18 22:17:47,920] [INFO] Selected 10 target genomes.
[2023-03-18 22:17:47,920] [INFO] Target genome list was writen to OceanDNA-b9687/target_genomes_gtdb.txt
[2023-03-18 22:17:47,930] [INFO] Task started: fastANI
[2023-03-18 22:17:47,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg31834626-f975-4516-b63d-8e9a1c520555/OceanDNA-b9687.fa --refList OceanDNA-b9687/target_genomes_gtdb.txt --output OceanDNA-b9687/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:17:56,917] [INFO] Task succeeded: fastANI
[2023-03-18 22:17:56,923] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:17:56,924] [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_003075045.1	s__Maribacter litoralis	97.4208	881	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	conclusive
GCF_001447995.1	s__Maribacter dokdonensis	84.2716	792	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_000744105.1	s__Maribacter forsetii	83.7416	710	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	83.4886	647	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	81.5137	628	959	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	81.4273	628	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155985.1	s__Maribacter ulvicola	81.4231	631	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	81.045	648	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_011050675.1	s__Maribacter sp011050675	80.7926	611	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900188415.1	s__Maribacter sedimenticola	79.1792	393	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:17:57,000] [INFO] GTDB search result was written to OceanDNA-b9687/result_gtdb.tsv
[2023-03-18 22:17:57,000] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:17:57,001] [INFO] DFAST_QC result json was written to OceanDNA-b9687/dqc_result.json
[2023-03-18 22:17:57,001] [INFO] DFAST_QC completed!
[2023-03-18 22:17:57,002] [INFO] Total running time: 0h1m37s