[2023-03-19 00:33:19,004] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,005] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference
[2023-03-19 00:33:20,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,132] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,133] [INFO] Running command: cat /var/lib/cwl/stg6f04c8dc-cce1-4c16-9a1d-56d9d1796519/OceanDNA-b23783.fa | prodigal -d OceanDNA-b23783/cds.fna -a OceanDNA-b23783/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:29,460] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:29,460] [INFO] Task started: HMMsearch
[2023-03-19 00:33:29,460] [INFO] Running command: hmmsearch --tblout OceanDNA-b23783/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/reference_markers.hmm OceanDNA-b23783/protein.faa > /dev/null
[2023-03-19 00:33:29,674] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:29,675] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6f04c8dc-cce1-4c16-9a1d-56d9d1796519/OceanDNA-b23783.fa]
[2023-03-19 00:33:29,705] [INFO] Query marker FASTA was written to OceanDNA-b23783/markers.fasta
[2023-03-19 00:33:29,707] [INFO] Task started: Blastn
[2023-03-19 00:33:29,707] [INFO] Running command: blastn -query OceanDNA-b23783/markers.fasta -db /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/reference_markers.fasta -out OceanDNA-b23783/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:30,271] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:30,288] [INFO] Selected 15 target genomes.
[2023-03-19 00:33:30,288] [INFO] Target genome list was writen to OceanDNA-b23783/target_genomes.txt
[2023-03-19 00:33:30,301] [INFO] Task started: fastANI
[2023-03-19 00:33:30,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f04c8dc-cce1-4c16-9a1d-56d9d1796519/OceanDNA-b23783.fa --refList OceanDNA-b23783/target_genomes.txt --output OceanDNA-b23783/fastani_result.tsv --threads 1
[2023-03-19 00:33:42,884] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:42,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:42,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:42,892] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:42,892] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:33:42,892] [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
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	82.0461	307	389	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	81.3385	309	389	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	81.0049	295	389	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.2467	165	389	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	77.7916	173	389	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.2961	125	389	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	77.2244	124	389	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	76.7404	86	389	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:33:42,896] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23783/tc_result.tsv
[2023-03-19 00:33:42,898] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:42,901] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:42,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/checkm_data
[2023-03-19 00:33:42,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:42,912] [INFO] Task started: CheckM
[2023-03-19 00:33:42,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23783/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23783/checkm_input OceanDNA-b23783/checkm_result
[2023-03-19 00:34:11,431] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:11,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.22%
Contamintation: 4.11%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-19 00:34:11,435] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:11,435] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:11,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23783/markers.fasta)
[2023-03-19 00:34:11,436] [INFO] Task started: Blastn
[2023-03-19 00:34:11,436] [INFO] Running command: blastn -query OceanDNA-b23783/markers.fasta -db /var/lib/cwl/stgd6f60613-aaee-4703-8284-6fd6d6f8759f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23783/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:12,226] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:12,230] [INFO] Selected 6 target genomes.
[2023-03-19 00:34:12,230] [INFO] Target genome list was writen to OceanDNA-b23783/target_genomes_gtdb.txt
[2023-03-19 00:34:12,261] [INFO] Task started: fastANI
[2023-03-19 00:34:12,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f04c8dc-cce1-4c16-9a1d-56d9d1796519/OceanDNA-b23783.fa --refList OceanDNA-b23783/target_genomes_gtdb.txt --output OceanDNA-b23783/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:15,887] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:15,891] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:34:15,892] [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_000961795.1	s__Hyphomonas sp000961795	97.1005	364	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018830285.1	s__Hyphomonas sp018830285	83.1336	329	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	82.0461	307	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	81.3385	309	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	81.128	298	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
GCF_000685275.1	s__Hyphomonas johnsonii	81.0049	295	389	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:15,893] [INFO] GTDB search result was written to OceanDNA-b23783/result_gtdb.tsv
[2023-03-19 00:34:15,895] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:15,897] [INFO] DFAST_QC result json was written to OceanDNA-b23783/dqc_result.json
[2023-03-19 00:34:15,897] [INFO] DFAST_QC completed!
[2023-03-19 00:34:15,897] [INFO] Total running time: 0h0m57s