[2023-03-18 23:11:06,937] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,937] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference
[2023-03-18 23:11:08,358] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,358] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,358] [INFO] Running command: cat /var/lib/cwl/stg0a03142b-bfed-4334-ad95-b7e4359f6916/OceanDNA-b33286.fa | prodigal -d OceanDNA-b33286/cds.fna -a OceanDNA-b33286/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:28,802] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:28,802] [INFO] Task started: HMMsearch
[2023-03-18 23:11:28,802] [INFO] Running command: hmmsearch --tblout OceanDNA-b33286/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/reference_markers.hmm OceanDNA-b33286/protein.faa > /dev/null
[2023-03-18 23:11:29,066] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:29,067] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a03142b-bfed-4334-ad95-b7e4359f6916/OceanDNA-b33286.fa]
[2023-03-18 23:11:29,090] [INFO] Query marker FASTA was written to OceanDNA-b33286/markers.fasta
[2023-03-18 23:11:29,091] [INFO] Task started: Blastn
[2023-03-18 23:11:29,091] [INFO] Running command: blastn -query OceanDNA-b33286/markers.fasta -db /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/reference_markers.fasta -out OceanDNA-b33286/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:29,898] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:29,899] [INFO] Selected 18 target genomes.
[2023-03-18 23:11:29,899] [INFO] Target genome list was writen to OceanDNA-b33286/target_genomes.txt
[2023-03-18 23:11:29,907] [INFO] Task started: fastANI
[2023-03-18 23:11:29,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a03142b-bfed-4334-ad95-b7e4359f6916/OceanDNA-b33286.fa --refList OceanDNA-b33286/target_genomes.txt --output OceanDNA-b33286/fastani_result.tsv --threads 1
[2023-03-18 23:11:47,139] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:47,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:47,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:47,150] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:11:47,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:11:47,151] [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
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	97.2616	795	903	95	conclusive
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	84.1925	628	903	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	84.0281	646	903	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	83.7537	628	903	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	83.3088	636	903	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	83.0241	565	903	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.7283	573	903	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.4203	525	903	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	80.9135	510	903	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	80.5742	465	903	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	80.5612	476	903	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	80.5048	507	903	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	80.3534	487	903	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.3375	482	903	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	79.0951	363	903	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.8609	316	903	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6418	369	903	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.5336	379	903	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:11:47,170] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33286/tc_result.tsv
[2023-03-18 23:11:47,170] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:47,170] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:47,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/checkm_data
[2023-03-18 23:11:47,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:47,178] [INFO] Task started: CheckM
[2023-03-18 23:11:47,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33286/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33286/checkm_input OceanDNA-b33286/checkm_result
[2023-03-18 23:12:38,149] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:38,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:38,152] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:38,152] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:38,153] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33286/markers.fasta)
[2023-03-18 23:12:38,153] [INFO] Task started: Blastn
[2023-03-18 23:12:38,153] [INFO] Running command: blastn -query OceanDNA-b33286/markers.fasta -db /var/lib/cwl/stg69597e84-529d-4e6d-a108-d77f61c6152b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33286/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:39,755] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:39,756] [INFO] Selected 16 target genomes.
[2023-03-18 23:12:39,756] [INFO] Target genome list was writen to OceanDNA-b33286/target_genomes_gtdb.txt
[2023-03-18 23:12:39,771] [INFO] Task started: fastANI
[2023-03-18 23:12:39,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a03142b-bfed-4334-ad95-b7e4359f6916/OceanDNA-b33286.fa --refList OceanDNA-b33286/target_genomes_gtdb.txt --output OceanDNA-b33286/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:54,920] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:54,929] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:54,930] [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_006716905.1	s__Acidovorax temperans	97.2616	795	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	96.32	95.61	0.84	0.79	8	conclusive
GCA_002377855.1	s__Acidovorax delafieldii_A	86.4379	640	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003669015.1	s__Acidovorax sp002754495	86.4268	693	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCF_003663825.1	s__Acidovorax sp003663825	86.185	688	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302535.1	s__Acidovorax sp000302535	84.3379	654	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.71	95.42	0.83	0.75	7	-
GCF_005405905.1	s__Acidovorax sp005405905	84.2216	650	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245625.1	s__Acidovorax kalamii	84.1858	629	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058055.1	s__Acidovorax sp003058055	84.1764	664	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.89	97.89	0.93	0.93	2	-
GCF_001633105.1	s__Acidovorax sp001633105	84.1193	673	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993815.1	s__Acidovorax delafieldii	84.0317	646	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.08	96.33	0.92	0.90	8	-
GCF_000238595.1	s__Acidovorax facilis	83.7804	612	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.91	97.91	0.86	0.86	2	-
GCF_003060895.1	s__Acidovorax sp003060895	83.5002	573	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464865.1	s__Acidovorax sp001464865	82.7148	544	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157145.1	s__Acidovorax carolinensis	82.7039	575	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCF_014207955.1	s__Acidovorax soli_A	82.6556	615	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	82.2157	636	903	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:54,930] [INFO] GTDB search result was written to OceanDNA-b33286/result_gtdb.tsv
[2023-03-18 23:12:54,930] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:54,932] [INFO] DFAST_QC result json was written to OceanDNA-b33286/dqc_result.json
[2023-03-18 23:12:54,932] [INFO] DFAST_QC completed!
[2023-03-18 23:12:54,932] [INFO] Total running time: 0h1m48s