[2023-03-18 01:41:22,935] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:22,935] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:22,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference
[2023-03-18 01:41:24,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:24,105] [INFO] Task started: Prodigal
[2023-03-18 01:41:24,105] [INFO] Running command: cat /var/lib/cwl/stgb2881a04-615c-4b20-82db-529d05569cfa/OceanDNA-b10365.fa | prodigal -d OceanDNA-b10365/cds.fna -a OceanDNA-b10365/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:44,391] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:44,391] [INFO] Task started: HMMsearch
[2023-03-18 01:41:44,391] [INFO] Running command: hmmsearch --tblout OceanDNA-b10365/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/reference_markers.hmm OceanDNA-b10365/protein.faa > /dev/null
[2023-03-18 01:41:44,616] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:44,616] [INFO] Found 6/6 markers.
[2023-03-18 01:41:44,639] [INFO] Query marker FASTA was written to OceanDNA-b10365/markers.fasta
[2023-03-18 01:41:44,640] [INFO] Task started: Blastn
[2023-03-18 01:41:44,640] [INFO] Running command: blastn -query OceanDNA-b10365/markers.fasta -db /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/reference_markers.fasta -out OceanDNA-b10365/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:45,247] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:45,248] [INFO] Selected 13 target genomes.
[2023-03-18 01:41:45,248] [INFO] Target genome list was writen to OceanDNA-b10365/target_genomes.txt
[2023-03-18 01:41:45,257] [INFO] Task started: fastANI
[2023-03-18 01:41:45,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2881a04-615c-4b20-82db-529d05569cfa/OceanDNA-b10365.fa --refList OceanDNA-b10365/target_genomes.txt --output OceanDNA-b10365/fastani_result.tsv --threads 1
[2023-03-18 01:41:55,432] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:55,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:55,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:55,441] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2023-03-18 01:41:55,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:41:55,442] [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
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	95.6691	885	1071	95	conclusive
Salegentibacter mishustinae	strain=KCTC 12263	GCA_001431365.1	270918	270918	type	True	95.6417	887	1071	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	95.5898	888	1071	95	conclusive
Salegentibacter mishustinae	strain=DSM 23404	GCA_003254095.1	270918	270918	type	True	95.5356	896	1071	95	conclusive
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	92.5089	797	1071	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	86.0768	781	1071	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	85.2269	768	1071	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	85.2093	763	1071	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	84.4969	742	1071	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	83.2494	745	1071	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.6489	61	1071	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3321	62	1071	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.891	82	1071	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:55,442] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10365/tc_result.tsv
[2023-03-18 01:41:55,442] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:55,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:55,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/checkm_data
[2023-03-18 01:41:55,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:55,447] [INFO] Task started: CheckM
[2023-03-18 01:41:55,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10365/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10365/checkm_input OceanDNA-b10365/checkm_result
[2023-03-18 01:42:46,928] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:46,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:46,931] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:46,931] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:46,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10365/markers.fasta)
[2023-03-18 01:42:46,932] [INFO] Task started: Blastn
[2023-03-18 01:42:46,933] [INFO] Running command: blastn -query OceanDNA-b10365/markers.fasta -db /var/lib/cwl/stg43b14485-1da4-452c-9278-932ef3c40eb1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10365/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:47,772] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:47,772] [INFO] Selected 7 target genomes.
[2023-03-18 01:42:47,772] [INFO] Target genome list was writen to OceanDNA-b10365/target_genomes_gtdb.txt
[2023-03-18 01:42:47,780] [INFO] Task started: fastANI
[2023-03-18 01:42:47,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2881a04-615c-4b20-82db-529d05569cfa/OceanDNA-b10365.fa --refList OceanDNA-b10365/target_genomes_gtdb.txt --output OceanDNA-b10365/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:53,742] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:53,747] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:42:53,747] [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_002900095.1	s__Salegentibacter mishustinae	95.6581	885	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	conclusive
GCF_900168265.1	s__Salegentibacter salarius	92.4288	795	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168045.1	s__Salegentibacter holothuriorum	87.0174	777	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	86.0885	780	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_000745315.1	s__Salegentibacter sp000745315	85.2664	806	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	85.2063	769	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900168115.1	s__Salegentibacter salinarum	83.4586	735	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:53,747] [INFO] GTDB search result was written to OceanDNA-b10365/result_gtdb.tsv
[2023-03-18 01:42:53,747] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:53,748] [INFO] DFAST_QC result json was written to OceanDNA-b10365/dqc_result.json
[2023-03-18 01:42:53,748] [INFO] DFAST_QC completed!
[2023-03-18 01:42:53,749] [INFO] Total running time: 0h1m31s