[2023-03-19 01:50:01,535] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,536] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference
[2023-03-19 01:50:02,652] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,653] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,653] [INFO] Running command: cat /var/lib/cwl/stg043a0007-2918-4aee-ae77-ecae9accbc22/OceanDNA-b38325.fa | prodigal -d OceanDNA-b38325/cds.fna -a OceanDNA-b38325/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:16,090] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:16,090] [INFO] Task started: HMMsearch
[2023-03-19 01:50:16,090] [INFO] Running command: hmmsearch --tblout OceanDNA-b38325/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/reference_markers.hmm OceanDNA-b38325/protein.faa > /dev/null
[2023-03-19 01:50:16,285] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:16,286] [INFO] Found 6/6 markers.
[2023-03-19 01:50:16,309] [INFO] Query marker FASTA was written to OceanDNA-b38325/markers.fasta
[2023-03-19 01:50:16,310] [INFO] Task started: Blastn
[2023-03-19 01:50:16,310] [INFO] Running command: blastn -query OceanDNA-b38325/markers.fasta -db /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/reference_markers.fasta -out OceanDNA-b38325/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:16,948] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:16,949] [INFO] Selected 18 target genomes.
[2023-03-19 01:50:16,950] [INFO] Target genome list was writen to OceanDNA-b38325/target_genomes.txt
[2023-03-19 01:50:16,962] [INFO] Task started: fastANI
[2023-03-19 01:50:16,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg043a0007-2918-4aee-ae77-ecae9accbc22/OceanDNA-b38325.fa --refList OceanDNA-b38325/target_genomes.txt --output OceanDNA-b38325/fastani_result.tsv --threads 1
[2023-03-19 01:50:28,368] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:28,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:28,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:28,379] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:28,379] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:28,379] [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 aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	88.3987	549	679	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	88.385	543	679	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	88.1855	559	679	95	below_threshold
Halomonas lionensis	strain=RHS90	GCA_002087295.1	1144478	1144478	type	True	88.123	548	679	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	87.943	642	679	95	below_threshold
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	87.912	640	679	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	86.2229	591	679	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	79.4383	356	679	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.3273	327	679	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	79.282	360	679	95	below_threshold
Halomonas massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	78.8288	261	679	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	78.7792	293	679	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	78.7577	288	679	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.6189	212	679	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.5989	218	679	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.5849	201	679	95	below_threshold
Larsenimonas salina	strain=CCM 8464	GCA_023736155.1	1295565	1295565	type	True	77.2255	64	679	95	below_threshold
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	76.8906	63	679	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:28,380] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38325/tc_result.tsv
[2023-03-19 01:50:28,380] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:28,380] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:28,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/checkm_data
[2023-03-19 01:50:28,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:28,385] [INFO] Task started: CheckM
[2023-03-19 01:50:28,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38325/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38325/checkm_input OceanDNA-b38325/checkm_result
[2023-03-19 01:51:05,378] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:05,378] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:05,380] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:05,380] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:05,381] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38325/markers.fasta)
[2023-03-19 01:51:05,381] [INFO] Task started: Blastn
[2023-03-19 01:51:05,382] [INFO] Running command: blastn -query OceanDNA-b38325/markers.fasta -db /var/lib/cwl/stg8251e593-6d4a-4526-af5c-db6f78e7ea3f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38325/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:06,302] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:06,303] [INFO] Selected 11 target genomes.
[2023-03-19 01:51:06,303] [INFO] Target genome list was writen to OceanDNA-b38325/target_genomes_gtdb.txt
[2023-03-19 01:51:06,308] [INFO] Task started: fastANI
[2023-03-19 01:51:06,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg043a0007-2918-4aee-ae77-ecae9accbc22/OceanDNA-b38325.fa --refList OceanDNA-b38325/target_genomes_gtdb.txt --output OceanDNA-b38325/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:14,998] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:15,005] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:51:15,005] [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_009846525.1	s__Halomonas sp002696125	98.5551	674	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	conclusive
GCF_900110265.1	s__Halomonas aquamarina	88.3987	549	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_002087295.1	s__Halomonas lionensis	88.123	548	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012427705.1	s__Halomonas piezotolerans	87.943	642	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_014640815.1	s__Halomonas lutescens	86.2074	592	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	82.2117	502	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000275725.1	s__Halomonas stevensii	82.0719	482	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_002211105.1	s__Halomonas campaniensis_A	79.6109	384	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCA_002366715.1	s__Halomonas sp002366715	79.5795	344	679	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	79.4384	356	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCF_013416325.1	s__Halomonas sedimenti	79.2815	360	679	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:15,005] [INFO] GTDB search result was written to OceanDNA-b38325/result_gtdb.tsv
[2023-03-19 01:51:15,005] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:15,007] [INFO] DFAST_QC result json was written to OceanDNA-b38325/dqc_result.json
[2023-03-19 01:51:15,007] [INFO] DFAST_QC completed!
[2023-03-19 01:51:15,007] [INFO] Total running time: 0h1m13s