[2023-03-15 09:25:29,060] [INFO] DFAST_QC pipeline started.
[2023-03-15 09:25:29,060] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 09:25:29,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference
[2023-03-15 09:25:30,381] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 09:25:30,382] [INFO] Task started: Prodigal
[2023-03-15 09:25:30,382] [INFO] Running command: cat /var/lib/cwl/stgf544ac8e-3cca-4bb1-8259-5564603584fb/OceanDNA-b6556.fa | prodigal -d OceanDNA-b6556/cds.fna -a OceanDNA-b6556/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:26:06,024] [INFO] Task succeeded: Prodigal
[2023-03-15 09:26:06,025] [INFO] Task started: HMMsearch
[2023-03-15 09:26:06,025] [INFO] Running command: hmmsearch --tblout OceanDNA-b6556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/reference_markers.hmm OceanDNA-b6556/protein.faa > /dev/null
[2023-03-15 09:26:06,252] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:26:06,252] [INFO] Found 6/6 markers.
[2023-03-15 09:26:06,279] [INFO] Query marker FASTA was written to OceanDNA-b6556/markers.fasta
[2023-03-15 09:26:06,279] [INFO] Task started: Blastn
[2023-03-15 09:26:06,279] [INFO] Running command: blastn -query OceanDNA-b6556/markers.fasta -db /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/reference_markers.fasta -out OceanDNA-b6556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:26:06,877] [INFO] Task succeeded: Blastn
[2023-03-15 09:26:06,878] [INFO] Selected 8 target genomes.
[2023-03-15 09:26:06,878] [INFO] Target genome list was writen to OceanDNA-b6556/target_genomes.txt
[2023-03-15 09:26:06,883] [INFO] Task started: fastANI
[2023-03-15 09:26:06,883] [INFO] Running command: fastANI --query /var/lib/cwl/stgf544ac8e-3cca-4bb1-8259-5564603584fb/OceanDNA-b6556.fa --refList OceanDNA-b6556/target_genomes.txt --output OceanDNA-b6556/fastani_result.tsv --threads 1
[2023-03-15 09:26:15,059] [INFO] Task succeeded: fastANI
[2023-03-15 09:26:15,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:26:15,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:26:15,065] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 09:26:15,065] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 09:26:15,065] [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
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	97.2726	1389	1587	95	conclusive
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	90.1132	1313	1587	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	87.8607	1290	1587	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	87.081	1200	1587	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	82.4285	1113	1587	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	75.9232	50	1587	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:26:15,065] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6556/tc_result.tsv
[2023-03-15 09:26:15,065] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:26:15,065] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:26:15,066] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/checkm_data
[2023-03-15 09:26:15,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:26:15,072] [INFO] Task started: CheckM
[2023-03-15 09:26:15,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6556/checkm_input OceanDNA-b6556/checkm_result
[2023-03-15 09:27:39,416] [INFO] Task succeeded: CheckM
[2023-03-15 09:27:39,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:27:39,420] [INFO] ===== Completeness check finished =====
[2023-03-15 09:27:39,420] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:27:39,420] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6556/markers.fasta)
[2023-03-15 09:27:39,421] [INFO] Task started: Blastn
[2023-03-15 09:27:39,421] [INFO] Running command: blastn -query OceanDNA-b6556/markers.fasta -db /var/lib/cwl/stgef251be7-ff40-435c-acab-d9e7531c7a8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:27:40,283] [INFO] Task succeeded: Blastn
[2023-03-15 09:27:40,284] [INFO] Selected 6 target genomes.
[2023-03-15 09:27:40,284] [INFO] Target genome list was writen to OceanDNA-b6556/target_genomes_gtdb.txt
[2023-03-15 09:27:40,345] [INFO] Task started: fastANI
[2023-03-15 09:27:40,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgf544ac8e-3cca-4bb1-8259-5564603584fb/OceanDNA-b6556.fa --refList OceanDNA-b6556/target_genomes_gtdb.txt --output OceanDNA-b6556/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:27:48,185] [INFO] Task succeeded: fastANI
[2023-03-15 09:27:48,189] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:27:48,189] [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_000733925.1	s__Arenibacter algicola	97.2591	1390	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	conclusive
GCF_003259375.1	s__Arenibacter echinorum	90.1189	1312	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860365.1	s__Arenibacter algicola_B	88.2356	1252	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129275.1	s__Arenibacter palladensis	87.869	1289	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	97.38	97.38	0.84	0.84	2	-
GCF_900177645.1	s__Arenibacter troitsensis	87.081	1200	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	85.0324	1168	1587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:27:48,189] [INFO] GTDB search result was written to OceanDNA-b6556/result_gtdb.tsv
[2023-03-15 09:27:48,189] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:27:48,190] [INFO] DFAST_QC result json was written to OceanDNA-b6556/dqc_result.json
[2023-03-15 09:27:48,190] [INFO] DFAST_QC completed!
[2023-03-15 09:27:48,190] [INFO] Total running time: 0h2m19s