[2023-03-18 07:29:30,339] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,340] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stgf9b76625-0f8f-49b6-bac2-242b6d0cb5b2/OceanDNA-b23530.fa | prodigal -d OceanDNA-b23530/cds.fna -a OceanDNA-b23530/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:50,733] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:50,733] [INFO] Task started: HMMsearch
[2023-03-18 07:29:50,733] [INFO] Running command: hmmsearch --tblout OceanDNA-b23530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/reference_markers.hmm OceanDNA-b23530/protein.faa > /dev/null
[2023-03-18 07:29:50,944] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:50,945] [INFO] Found 6/6 markers.
[2023-03-18 07:29:50,965] [INFO] Query marker FASTA was written to OceanDNA-b23530/markers.fasta
[2023-03-18 07:29:50,965] [INFO] Task started: Blastn
[2023-03-18 07:29:50,965] [INFO] Running command: blastn -query OceanDNA-b23530/markers.fasta -db /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/reference_markers.fasta -out OceanDNA-b23530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:51,722] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:51,723] [INFO] Selected 16 target genomes.
[2023-03-18 07:29:51,723] [INFO] Target genome list was writen to OceanDNA-b23530/target_genomes.txt
[2023-03-18 07:29:51,731] [INFO] Task started: fastANI
[2023-03-18 07:29:51,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b76625-0f8f-49b6-bac2-242b6d0cb5b2/OceanDNA-b23530.fa --refList OceanDNA-b23530/target_genomes.txt --output OceanDNA-b23530/fastani_result.tsv --threads 1
[2023-03-18 07:30:04,202] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:04,202] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:04,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:04,211] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:04,211] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:04,212] [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
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	81.5552	688	1007	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	81.3018	665	1007	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	80.7177	641	1007	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	80.1541	552	1007	95	below_threshold
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	79.867	514	1007	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	79.2647	498	1007	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	79.1286	440	1007	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.4026	67	1007	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	76.33	82	1007	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.3053	71	1007	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	76.0135	74	1007	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.9461	71	1007	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	75.7464	61	1007	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	75.7028	52	1007	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.6305	74	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:04,212] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23530/tc_result.tsv
[2023-03-18 07:30:04,212] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:04,212] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:04,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/checkm_data
[2023-03-18 07:30:04,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:04,217] [INFO] Task started: CheckM
[2023-03-18 07:30:04,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23530/checkm_input OceanDNA-b23530/checkm_result
[2023-03-18 07:30:52,229] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:52,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:52,231] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:52,232] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:52,232] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23530/markers.fasta)
[2023-03-18 07:30:52,232] [INFO] Task started: Blastn
[2023-03-18 07:30:52,232] [INFO] Running command: blastn -query OceanDNA-b23530/markers.fasta -db /var/lib/cwl/stg02fbaa40-6c78-45d2-be99-eeb786aba95e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:53,635] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:53,635] [INFO] Selected 11 target genomes.
[2023-03-18 07:30:53,636] [INFO] Target genome list was writen to OceanDNA-b23530/target_genomes_gtdb.txt
[2023-03-18 07:30:53,771] [INFO] Task started: fastANI
[2023-03-18 07:30:53,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b76625-0f8f-49b6-bac2-242b6d0cb5b2/OceanDNA-b23530.fa --refList OceanDNA-b23530/target_genomes_gtdb.txt --output OceanDNA-b23530/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:01,431] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:01,438] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:01,438] [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_002733705.1	s__Henriciella sp002733705	99.6718	850	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.60	99.22	0.83	0.79	5	conclusive
GCF_003576245.1	s__Henriciella algicola	81.5448	689	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960415.1	s__Henriciella sp012960415	81.5	658	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	99.93	99.93	0.95	0.95	2	-
GCF_000376805.1	s__Henriciella marina	81.3119	664	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576345.1	s__Henriciella barbarensis	80.7177	641	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	80.1438	553	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576285.1	s__Henriciella sp003576285	79.8359	503	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCF_002088935.1	s__Henriciella litoralis	79.2597	498	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009909065.1	s__UBA5336 sp009909065	76.6807	169	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	75.7997	77	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004634425.1	s__Terricaulis sp004634425	75.61	58	1007	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__TH1-2;g__Terricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:01,438] [INFO] GTDB search result was written to OceanDNA-b23530/result_gtdb.tsv
[2023-03-18 07:31:01,438] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:01,440] [INFO] DFAST_QC result json was written to OceanDNA-b23530/dqc_result.json
[2023-03-18 07:31:01,440] [INFO] DFAST_QC completed!
[2023-03-18 07:31:01,440] [INFO] Total running time: 0h1m31s