[2023-03-18 01:08:39,205] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,205] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,205] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference
[2023-03-18 01:08:40,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,383] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,384] [INFO] Running command: cat /var/lib/cwl/stg9e23e2e4-35a4-4a3e-bfa3-75c4c53e1d04/OceanDNA-b38322.fa | prodigal -d OceanDNA-b38322/cds.fna -a OceanDNA-b38322/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:09:01,946] [INFO] Task succeeded: Prodigal
[2023-03-18 01:09:01,947] [INFO] Task started: HMMsearch
[2023-03-18 01:09:01,947] [INFO] Running command: hmmsearch --tblout OceanDNA-b38322/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/reference_markers.hmm OceanDNA-b38322/protein.faa > /dev/null
[2023-03-18 01:09:02,174] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:09:02,175] [INFO] Found 6/6 markers.
[2023-03-18 01:09:02,202] [INFO] Query marker FASTA was written to OceanDNA-b38322/markers.fasta
[2023-03-18 01:09:02,204] [INFO] Task started: Blastn
[2023-03-18 01:09:02,204] [INFO] Running command: blastn -query OceanDNA-b38322/markers.fasta -db /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/reference_markers.fasta -out OceanDNA-b38322/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:02,851] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:02,853] [INFO] Selected 11 target genomes.
[2023-03-18 01:09:02,853] [INFO] Target genome list was writen to OceanDNA-b38322/target_genomes.txt
[2023-03-18 01:09:02,860] [INFO] Task started: fastANI
[2023-03-18 01:09:02,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e23e2e4-35a4-4a3e-bfa3-75c4c53e1d04/OceanDNA-b38322.fa --refList OceanDNA-b38322/target_genomes.txt --output OceanDNA-b38322/fastani_result.tsv --threads 1
[2023-03-18 01:09:11,790] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:11,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:11,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:11,799] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:11,799] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:11,799] [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	86.7873	935	1198	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	85.7154	933	1198	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	83.2997	861	1198	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	83.2541	874	1198	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	82.522	783	1198	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	82.5008	786	1198	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	80.5035	608	1198	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	80.4476	608	1198	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.778	428	1198	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.979	180	1198	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.8472	191	1198	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:11,800] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38322/tc_result.tsv
[2023-03-18 01:09:11,800] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:11,801] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:11,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/checkm_data
[2023-03-18 01:09:11,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:11,809] [INFO] Task started: CheckM
[2023-03-18 01:09:11,809] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38322/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38322/checkm_input OceanDNA-b38322/checkm_result
[2023-03-18 01:10:06,134] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:06,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.63%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:06,138] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:06,138] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:06,139] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38322/markers.fasta)
[2023-03-18 01:10:06,140] [INFO] Task started: Blastn
[2023-03-18 01:10:06,140] [INFO] Running command: blastn -query OceanDNA-b38322/markers.fasta -db /var/lib/cwl/stgf1292d5e-c2f0-43eb-babf-066c8b4d6f54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38322/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:07,229] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:07,231] [INFO] Selected 12 target genomes.
[2023-03-18 01:10:07,231] [INFO] Target genome list was writen to OceanDNA-b38322/target_genomes_gtdb.txt
[2023-03-18 01:10:07,243] [INFO] Task started: fastANI
[2023-03-18 01:10:07,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e23e2e4-35a4-4a3e-bfa3-75c4c53e1d04/OceanDNA-b38322.fa --refList OceanDNA-b38322/target_genomes_gtdb.txt --output OceanDNA-b38322/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:18,713] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:18,720] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:10:18,721] [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_002366715.1	s__Halomonas sp002366715	97.1819	1045	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013371085.1	s__Halomonas maris	86.7873	935	1198	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	85.7154	933	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCF_000235725.1	s__Halomonas sp000235725	85.4711	883	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCA_007182875.1	s__Halomonas sulfidaeris	84.6376	881	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.07	97.07	0.89	0.89	2	-
GCF_000336575.1	s__Halomonas titanicae	83.3052	860	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_013416325.1	s__Halomonas sedimenti	83.2614	873	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_004364445.1	s__Halomonas alkaliantarctica	82.9911	855	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_001882345.1	s__Halomonas sp001882345	82.986	842	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257525.1	s__Halomonas ventosae_B	82.8481	888	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_002211105.1	s__Halomonas campaniensis_A	82.548	833	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_000236035.1	s__Halomonas boliviensis	82.5008	786	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:18,722] [INFO] GTDB search result was written to OceanDNA-b38322/result_gtdb.tsv
[2023-03-18 01:10:18,722] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:18,724] [INFO] DFAST_QC result json was written to OceanDNA-b38322/dqc_result.json
[2023-03-18 01:10:18,724] [INFO] DFAST_QC completed!
[2023-03-18 01:10:18,724] [INFO] Total running time: 0h1m40s