[2023-03-17 23:08:31,933] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,933] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference
[2023-03-17 23:08:33,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,083] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,083] [INFO] Running command: cat /var/lib/cwl/stg0407898d-b4df-4a48-9153-2815af35a127/OceanDNA-b23819.fa | prodigal -d OceanDNA-b23819/cds.fna -a OceanDNA-b23819/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:54,269] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:54,270] [INFO] Task started: HMMsearch
[2023-03-17 23:08:54,270] [INFO] Running command: hmmsearch --tblout OceanDNA-b23819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/reference_markers.hmm OceanDNA-b23819/protein.faa > /dev/null
[2023-03-17 23:08:54,500] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:54,501] [INFO] Found 6/6 markers.
[2023-03-17 23:08:54,526] [INFO] Query marker FASTA was written to OceanDNA-b23819/markers.fasta
[2023-03-17 23:08:54,527] [INFO] Task started: Blastn
[2023-03-17 23:08:54,527] [INFO] Running command: blastn -query OceanDNA-b23819/markers.fasta -db /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/reference_markers.fasta -out OceanDNA-b23819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:55,199] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:55,204] [INFO] Selected 24 target genomes.
[2023-03-17 23:08:55,204] [INFO] Target genome list was writen to OceanDNA-b23819/target_genomes.txt
[2023-03-17 23:08:55,217] [INFO] Task started: fastANI
[2023-03-17 23:08:55,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg0407898d-b4df-4a48-9153-2815af35a127/OceanDNA-b23819.fa --refList OceanDNA-b23819/target_genomes.txt --output OceanDNA-b23819/fastani_result.tsv --threads 1
[2023-03-17 23:09:10,571] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:10,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:10,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:10,578] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:10,578] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:09:10,578] [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
Ponticaulis koreensis	strain=DSM 19734	GCA_000420665.1	1123045	1123045	type	True	77.2279	244	1142	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.2856	77	1142	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.2419	76	1142	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	76.1676	65	1142	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.1403	61	1142	95	below_threshold
Henriciella litoralis	strain=DSM 22014	GCA_002088935.1	568102	568102	type	True	76.1122	81	1142	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	76.0616	81	1142	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	76.0066	62	1142	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	75.7996	63	1142	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:09:10,579] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23819/tc_result.tsv
[2023-03-17 23:09:10,581] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:10,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:10,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/checkm_data
[2023-03-17 23:09:10,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:10,600] [INFO] Task started: CheckM
[2023-03-17 23:09:10,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23819/checkm_input OceanDNA-b23819/checkm_result
[2023-03-17 23:10:04,783] [INFO] Task succeeded: CheckM
[2023-03-17 23:10:04,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:10:04,804] [INFO] ===== Completeness check finished =====
[2023-03-17 23:10:04,804] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:10:04,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23819/markers.fasta)
[2023-03-17 23:10:04,805] [INFO] Task started: Blastn
[2023-03-17 23:10:04,806] [INFO] Running command: blastn -query OceanDNA-b23819/markers.fasta -db /var/lib/cwl/stg88100bd4-f01e-4719-9a85-8eef47eaaa1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:05,996] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:06,016] [INFO] Selected 16 target genomes.
[2023-03-17 23:10:06,016] [INFO] Target genome list was writen to OceanDNA-b23819/target_genomes_gtdb.txt
[2023-03-17 23:10:06,028] [INFO] Task started: fastANI
[2023-03-17 23:10:06,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg0407898d-b4df-4a48-9153-2815af35a127/OceanDNA-b23819.fa --refList OceanDNA-b23819/target_genomes_gtdb.txt --output OceanDNA-b23819/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:17,743] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:17,750] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:10:17,750] [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_002692725.1	s__Ponticaulis sp002692725	99.9929	1102	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002701295.1	s__Ponticaulis sp002701295	78.0217	298	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002173095.1	s__Ponticaulis sp002173095	77.8519	276	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002699325.1	s__Ponticaulis sp002699325	77.5599	266	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723155.1	s__Ponticaulis sp002723155	77.4138	243	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.28	99.28	0.86	0.86	2	-
GCF_000420665.1	s__Ponticaulis koreensis	77.2178	245	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338565.1	s__Ponticaulis sp002338565	77.1754	263	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Ponticaulis	95.0	99.94	99.86	0.98	0.96	4	-
GCF_000682675.1	s__Hyphomonas pacifica	76.1676	65	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCF_000685295.1	s__Hyphomonas oceanitis	76.0066	62	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854405.1	s__Henriciella sp001854405	75.9961	75	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:10:17,755] [INFO] GTDB search result was written to OceanDNA-b23819/result_gtdb.tsv
[2023-03-17 23:10:17,755] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:17,757] [INFO] DFAST_QC result json was written to OceanDNA-b23819/dqc_result.json
[2023-03-17 23:10:17,757] [INFO] DFAST_QC completed!
[2023-03-17 23:10:17,757] [INFO] Total running time: 0h1m46s