[2023-03-15 04:59:01,512] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:59:01,514] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:59:01,514] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference
[2023-03-15 04:59:03,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:59:03,421] [INFO] Task started: Prodigal
[2023-03-15 04:59:03,422] [INFO] Running command: cat /var/lib/cwl/stgd07d94f3-5197-44c7-89a5-7a866e12e94c/OceanDNA-b44686.fa | prodigal -d OceanDNA-b44686/cds.fna -a OceanDNA-b44686/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:59:22,983] [INFO] Task succeeded: Prodigal
[2023-03-15 04:59:22,983] [INFO] Task started: HMMsearch
[2023-03-15 04:59:22,983] [INFO] Running command: hmmsearch --tblout OceanDNA-b44686/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/reference_markers.hmm OceanDNA-b44686/protein.faa > /dev/null
[2023-03-15 04:59:23,261] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:59:23,262] [INFO] Found 6/6 markers.
[2023-03-15 04:59:23,289] [INFO] Query marker FASTA was written to OceanDNA-b44686/markers.fasta
[2023-03-15 04:59:23,290] [INFO] Task started: Blastn
[2023-03-15 04:59:23,290] [INFO] Running command: blastn -query OceanDNA-b44686/markers.fasta -db /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/reference_markers.fasta -out OceanDNA-b44686/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:59:24,234] [INFO] Task succeeded: Blastn
[2023-03-15 04:59:24,239] [INFO] Selected 11 target genomes.
[2023-03-15 04:59:24,239] [INFO] Target genome list was writen to OceanDNA-b44686/target_genomes.txt
[2023-03-15 04:59:24,245] [INFO] Task started: fastANI
[2023-03-15 04:59:24,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07d94f3-5197-44c7-89a5-7a866e12e94c/OceanDNA-b44686.fa --refList OceanDNA-b44686/target_genomes.txt --output OceanDNA-b44686/fastani_result.tsv --threads 1
[2023-03-15 04:59:32,397] [INFO] Task succeeded: fastANI
[2023-03-15 04:59:32,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:59:32,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:59:32,406] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:59:32,406] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:59:32,406] [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
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	89.4956	823	996	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	87.7977	803	996	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	86.6059	759	996	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	86.2701	712	996	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	84.7563	742	996	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	84.4998	733	996	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	82.5243	643	996	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	82.4572	628	996	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.1074	416	996	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.0925	446	996	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.3859	489	996	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:59:32,408] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44686/tc_result.tsv
[2023-03-15 04:59:32,408] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:59:32,408] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:59:32,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/checkm_data
[2023-03-15 04:59:32,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:59:32,418] [INFO] Task started: CheckM
[2023-03-15 04:59:32,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44686/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44686/checkm_input OceanDNA-b44686/checkm_result
[2023-03-15 05:00:27,713] [INFO] Task succeeded: CheckM
[2023-03-15 05:00:27,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:00:27,727] [INFO] ===== Completeness check finished =====
[2023-03-15 05:00:27,727] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:00:27,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44686/markers.fasta)
[2023-03-15 05:00:27,728] [INFO] Task started: Blastn
[2023-03-15 05:00:27,728] [INFO] Running command: blastn -query OceanDNA-b44686/markers.fasta -db /var/lib/cwl/stgdf490494-8071-4896-812d-1b5a09fa85d6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44686/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:29,606] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:29,609] [INFO] Selected 9 target genomes.
[2023-03-15 05:00:29,609] [INFO] Target genome list was writen to OceanDNA-b44686/target_genomes_gtdb.txt
[2023-03-15 05:00:29,673] [INFO] Task started: fastANI
[2023-03-15 05:00:29,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgd07d94f3-5197-44c7-89a5-7a866e12e94c/OceanDNA-b44686.fa --refList OceanDNA-b44686/target_genomes_gtdb.txt --output OceanDNA-b44686/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:00:36,614] [INFO] Task succeeded: fastANI
[2023-03-15 05:00:36,620] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:00:36,620] [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_014643775.1	s__Arenimonas soli	89.5138	822	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743535.1	s__Arenimonas donghaensis	87.7977	803	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024235.1	s__Arenimonas caeni	86.638	757	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724815.1	s__Arenimonas sp001724815	86.4116	758	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	86.2696	712	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	85.5117	545	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_007993735.1	s__Arenimonas daejeonensis	84.3508	698	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241895.1	s__Arenimonas sp003241895	83.2234	696	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	80.2603	469	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:00:36,622] [INFO] GTDB search result was written to OceanDNA-b44686/result_gtdb.tsv
[2023-03-15 05:00:36,625] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:00:36,628] [INFO] DFAST_QC result json was written to OceanDNA-b44686/dqc_result.json
[2023-03-15 05:00:36,628] [INFO] DFAST_QC completed!
[2023-03-15 05:00:36,628] [INFO] Total running time: 0h1m35s