[2023-03-19 04:29:38,147] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:38,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:38,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference
[2023-03-19 04:29:39,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:39,833] [INFO] Task started: Prodigal
[2023-03-19 04:29:39,833] [INFO] Running command: cat /var/lib/cwl/stg3d470097-26ed-475a-ba86-fb43dd84ce09/OceanDNA-b44690.fa | prodigal -d OceanDNA-b44690/cds.fna -a OceanDNA-b44690/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:56,511] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:56,511] [INFO] Task started: HMMsearch
[2023-03-19 04:29:56,511] [INFO] Running command: hmmsearch --tblout OceanDNA-b44690/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/reference_markers.hmm OceanDNA-b44690/protein.faa > /dev/null
[2023-03-19 04:29:56,723] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:56,724] [INFO] Found 6/6 markers.
[2023-03-19 04:29:56,742] [INFO] Query marker FASTA was written to OceanDNA-b44690/markers.fasta
[2023-03-19 04:29:56,742] [INFO] Task started: Blastn
[2023-03-19 04:29:56,742] [INFO] Running command: blastn -query OceanDNA-b44690/markers.fasta -db /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/reference_markers.fasta -out OceanDNA-b44690/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:57,634] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:57,635] [INFO] Selected 15 target genomes.
[2023-03-19 04:29:57,635] [INFO] Target genome list was writen to OceanDNA-b44690/target_genomes.txt
[2023-03-19 04:29:57,642] [INFO] Task started: fastANI
[2023-03-19 04:29:57,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d470097-26ed-475a-ba86-fb43dd84ce09/OceanDNA-b44690.fa --refList OceanDNA-b44690/target_genomes.txt --output OceanDNA-b44690/fastani_result.tsv --threads 1
[2023-03-19 04:30:08,144] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:08,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:08,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:08,154] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:08,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:08,154] [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 metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	92.5248	755	901	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	86.4956	631	901	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	86.2378	719	901	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	85.7718	652	901	95	below_threshold
Arenimonas soli	strain=CGMCC 1.15905	GCA_014643775.1	2269504	2269504	type	True	84.6994	673	901	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	83.3407	611	901	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	83.1983	611	901	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.5626	414	901	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.4314	482	901	95	below_threshold
Arenimonas oryziterrae	strain=YC6267	GCA_000747135.1	498055	498055	type	True	80.1882	476	901	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	80.1794	481	901	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	79.972	463	901	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	79.7236	488	901	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	79.5787	381	901	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	79.4017	399	901	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:08,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44690/tc_result.tsv
[2023-03-19 04:30:08,155] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:08,155] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:08,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/checkm_data
[2023-03-19 04:30:08,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:08,160] [INFO] Task started: CheckM
[2023-03-19 04:30:08,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44690/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44690/checkm_input OceanDNA-b44690/checkm_result
[2023-03-19 04:30:52,730] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:52,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:52,733] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:52,733] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:52,734] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44690/markers.fasta)
[2023-03-19 04:30:52,734] [INFO] Task started: Blastn
[2023-03-19 04:30:52,734] [INFO] Running command: blastn -query OceanDNA-b44690/markers.fasta -db /var/lib/cwl/stgbcef3be1-7537-4261-9b6f-d09721b996d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44690/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:54,629] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:54,630] [INFO] Selected 11 target genomes.
[2023-03-19 04:30:54,630] [INFO] Target genome list was writen to OceanDNA-b44690/target_genomes_gtdb.txt
[2023-03-19 04:30:54,642] [INFO] Task started: fastANI
[2023-03-19 04:30:54,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d470097-26ed-475a-ba86-fb43dd84ce09/OceanDNA-b44690.fa --refList OceanDNA-b44690/target_genomes_gtdb.txt --output OceanDNA-b44690/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:31:02,594] [INFO] Task succeeded: fastANI
[2023-03-19 04:31:02,601] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:31:02,602] [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_000747155.1	s__Arenimonas metalli	92.5412	754	901	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	86.5107	629	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265115.1	s__Arenimonas terrae	86.2104	721	901	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	86.0696	690	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993735.1	s__Arenimonas daejeonensis	85.8028	667	901	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	85.7718	652	901	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	85.5087	490	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCA_003241895.1	s__Arenimonas sp003241895	85.452	678	901	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	84.2502	656	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	83.3114	613	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_009496535.1	s__Stenotrophomonas sp003504055	79.9092	486	901	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	96.53	96.53	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:31:02,602] [INFO] GTDB search result was written to OceanDNA-b44690/result_gtdb.tsv
[2023-03-19 04:31:02,602] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:31:02,603] [INFO] DFAST_QC result json was written to OceanDNA-b44690/dqc_result.json
[2023-03-19 04:31:02,604] [INFO] DFAST_QC completed!
[2023-03-19 04:31:02,604] [INFO] Total running time: 0h1m24s