[2023-03-16 20:25:54,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:25:54,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:25:54,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference
[2023-03-16 20:25:55,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:25:55,949] [INFO] Task started: Prodigal
[2023-03-16 20:25:55,949] [INFO] Running command: cat /var/lib/cwl/stgfadbb7c5-bf86-46e5-ac8e-82f977c0940a/OceanDNA-b38308.fa | prodigal -d OceanDNA-b38308/cds.fna -a OceanDNA-b38308/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:26:17,167] [INFO] Task succeeded: Prodigal
[2023-03-16 20:26:17,167] [INFO] Task started: HMMsearch
[2023-03-16 20:26:17,168] [INFO] Running command: hmmsearch --tblout OceanDNA-b38308/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/reference_markers.hmm OceanDNA-b38308/protein.faa > /dev/null
[2023-03-16 20:26:17,420] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:26:17,421] [INFO] Found 6/6 markers.
[2023-03-16 20:26:17,447] [INFO] Query marker FASTA was written to OceanDNA-b38308/markers.fasta
[2023-03-16 20:26:17,448] [INFO] Task started: Blastn
[2023-03-16 20:26:17,448] [INFO] Running command: blastn -query OceanDNA-b38308/markers.fasta -db /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/reference_markers.fasta -out OceanDNA-b38308/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:26:18,155] [INFO] Task succeeded: Blastn
[2023-03-16 20:26:18,156] [INFO] Selected 11 target genomes.
[2023-03-16 20:26:18,156] [INFO] Target genome list was writen to OceanDNA-b38308/target_genomes.txt
[2023-03-16 20:26:18,161] [INFO] Task started: fastANI
[2023-03-16 20:26:18,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgfadbb7c5-bf86-46e5-ac8e-82f977c0940a/OceanDNA-b38308.fa --refList OceanDNA-b38308/target_genomes.txt --output OceanDNA-b38308/fastani_result.tsv --threads 1
[2023-03-16 20:26:31,110] [INFO] Task succeeded: fastANI
[2023-03-16 20:26:31,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:26:31,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:26:31,119] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:26:31,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:26:31,119] [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
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	94.609	995	1186	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	92.3237	951	1186	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	85.2815	892	1186	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	85.1069	883	1186	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	84.0337	807	1186	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	83.9588	822	1186	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.0357	629	1186	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.0303	623	1186	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.0675	428	1186	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.3427	202	1186	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.3096	183	1186	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:26:31,120] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38308/tc_result.tsv
[2023-03-16 20:26:31,120] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:26:31,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:26:31,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/checkm_data
[2023-03-16 20:26:31,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:26:31,353] [INFO] Task started: CheckM
[2023-03-16 20:26:31,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38308/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38308/checkm_input OceanDNA-b38308/checkm_result
[2023-03-16 20:27:44,183] [INFO] Task succeeded: CheckM
[2023-03-16 20:27:44,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.09%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 20:27:44,187] [INFO] ===== Completeness check finished =====
[2023-03-16 20:27:44,187] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:27:44,188] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38308/markers.fasta)
[2023-03-16 20:27:44,189] [INFO] Task started: Blastn
[2023-03-16 20:27:44,189] [INFO] Running command: blastn -query OceanDNA-b38308/markers.fasta -db /var/lib/cwl/stg1889245c-c11f-44e8-9e93-4d1c304fe4c4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38308/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:27:45,587] [INFO] Task succeeded: Blastn
[2023-03-16 20:27:45,588] [INFO] Selected 9 target genomes.
[2023-03-16 20:27:45,589] [INFO] Target genome list was writen to OceanDNA-b38308/target_genomes_gtdb.txt
[2023-03-16 20:27:45,598] [INFO] Task started: fastANI
[2023-03-16 20:27:45,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgfadbb7c5-bf86-46e5-ac8e-82f977c0940a/OceanDNA-b38308.fa --refList OceanDNA-b38308/target_genomes_gtdb.txt --output OceanDNA-b38308/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:28:01,075] [INFO] Task succeeded: fastANI
[2023-03-16 20:28:01,081] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 20:28:01,082] [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_000235725.1	s__Halomonas sp000235725	96.6158	957	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	conclusive
GCF_013371085.1	s__Halomonas maris	94.609	995	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415125.1	s__Halomonas glaciei	92.3237	951	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCA_002366715.1	s__Halomonas sp002366715	86.2244	885	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336575.1	s__Halomonas titanicae	85.276	893	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_001882345.1	s__Halomonas sp001882345	85.2227	844	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364445.1	s__Halomonas alkaliantarctica	84.7502	909	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_002257525.1	s__Halomonas ventosae_B	84.6452	907	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	83.9588	822	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-16 20:28:01,082] [INFO] GTDB search result was written to OceanDNA-b38308/result_gtdb.tsv
[2023-03-16 20:28:01,082] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:28:01,084] [INFO] DFAST_QC result json was written to OceanDNA-b38308/dqc_result.json
[2023-03-16 20:28:01,084] [INFO] DFAST_QC completed!
[2023-03-16 20:28:01,084] [INFO] Total running time: 0h2m6s