[2023-03-15 11:09:10,892] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,892] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference
[2023-03-15 11:09:12,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,095] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,095] [INFO] Running command: cat /var/lib/cwl/stg987f3d48-2c9a-4c3f-bfa7-74848b931e0f/OceanDNA-b44684.fa | prodigal -d OceanDNA-b44684/cds.fna -a OceanDNA-b44684/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:29,842] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:29,843] [INFO] Task started: HMMsearch
[2023-03-15 11:09:29,843] [INFO] Running command: hmmsearch --tblout OceanDNA-b44684/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/reference_markers.hmm OceanDNA-b44684/protein.faa > /dev/null
[2023-03-15 11:09:30,098] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:30,099] [INFO] Found 6/6 markers.
[2023-03-15 11:09:30,118] [INFO] Query marker FASTA was written to OceanDNA-b44684/markers.fasta
[2023-03-15 11:09:30,119] [INFO] Task started: Blastn
[2023-03-15 11:09:30,119] [INFO] Running command: blastn -query OceanDNA-b44684/markers.fasta -db /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/reference_markers.fasta -out OceanDNA-b44684/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:31,002] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:31,003] [INFO] Selected 11 target genomes.
[2023-03-15 11:09:31,003] [INFO] Target genome list was writen to OceanDNA-b44684/target_genomes.txt
[2023-03-15 11:09:31,009] [INFO] Task started: fastANI
[2023-03-15 11:09:31,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg987f3d48-2c9a-4c3f-bfa7-74848b931e0f/OceanDNA-b44684.fa --refList OceanDNA-b44684/target_genomes.txt --output OceanDNA-b44684/fastani_result.tsv --threads 1
[2023-03-15 11:09:39,655] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:39,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:39,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:39,662] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:39,663] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:39,663] [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	91.906	790	947	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	88.6739	786	947	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	87.5758	689	947	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	87.2761	725	947	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	85.6205	730	947	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	85.0874	716	947	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	82.727	613	947	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	82.6889	630	947	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.1941	421	947	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	79.6432	469	947	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	79.4688	403	947	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:39,663] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44684/tc_result.tsv
[2023-03-15 11:09:39,663] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:39,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:39,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/checkm_data
[2023-03-15 11:09:39,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:39,669] [INFO] Task started: CheckM
[2023-03-15 11:09:39,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44684/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44684/checkm_input OceanDNA-b44684/checkm_result
[2023-03-15 11:10:27,733] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:27,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:27,736] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:27,736] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:27,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44684/markers.fasta)
[2023-03-15 11:10:27,736] [INFO] Task started: Blastn
[2023-03-15 11:10:27,736] [INFO] Running command: blastn -query OceanDNA-b44684/markers.fasta -db /var/lib/cwl/stg9f1f0d88-ab39-4808-a505-ede323bbef39/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44684/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:29,267] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:29,268] [INFO] Selected 9 target genomes.
[2023-03-15 11:10:29,268] [INFO] Target genome list was writen to OceanDNA-b44684/target_genomes_gtdb.txt
[2023-03-15 11:10:29,275] [INFO] Task started: fastANI
[2023-03-15 11:10:29,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg987f3d48-2c9a-4c3f-bfa7-74848b931e0f/OceanDNA-b44684.fa --refList OceanDNA-b44684/target_genomes_gtdb.txt --output OceanDNA-b44684/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:35,995] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:36,001] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:36,001] [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	91.906	790	947	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	88.6702	787	947	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	87.5758	689	947	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	87.4067	721	947	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	87.2554	726	947	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	86.4926	541	947	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_000747155.1	s__Arenimonas metalli	85.6269	729	947	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	84.0738	673	947	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	80.3078	465	947	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 11:10:36,001] [INFO] GTDB search result was written to OceanDNA-b44684/result_gtdb.tsv
[2023-03-15 11:10:36,001] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:36,002] [INFO] DFAST_QC result json was written to OceanDNA-b44684/dqc_result.json
[2023-03-15 11:10:36,002] [INFO] DFAST_QC completed!
[2023-03-15 11:10:36,002] [INFO] Total running time: 0h1m25s