[2023-06-28 13:31:21,218] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:21,220] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:21,220] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference
[2023-06-28 13:31:22,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:22,378] [INFO] Task started: Prodigal
[2023-06-28 13:31:22,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b9b577a-441e-4001-8a1d-9a0a444cc88c/GCA_017983755.1_ASM1798375v1_genomic.fna.gz | prodigal -d GCA_017983755.1_ASM1798375v1_genomic.fna/cds.fna -a GCA_017983755.1_ASM1798375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:28,796] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:28,796] [INFO] Task started: HMMsearch
[2023-06-28 13:31:28,796] [INFO] Running command: hmmsearch --tblout GCA_017983755.1_ASM1798375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/reference_markers.hmm GCA_017983755.1_ASM1798375v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:28,958] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:28,959] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7b9b577a-441e-4001-8a1d-9a0a444cc88c/GCA_017983755.1_ASM1798375v1_genomic.fna.gz]
[2023-06-28 13:31:28,982] [INFO] Query marker FASTA was written to GCA_017983755.1_ASM1798375v1_genomic.fna/markers.fasta
[2023-06-28 13:31:28,982] [INFO] Task started: Blastn
[2023-06-28 13:31:28,982] [INFO] Running command: blastn -query GCA_017983755.1_ASM1798375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/reference_markers.fasta -out GCA_017983755.1_ASM1798375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:29,666] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:29,669] [INFO] Selected 8 target genomes.
[2023-06-28 13:31:29,669] [INFO] Target genome list was writen to GCA_017983755.1_ASM1798375v1_genomic.fna/target_genomes.txt
[2023-06-28 13:31:29,670] [INFO] Task started: fastANI
[2023-06-28 13:31:29,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9b577a-441e-4001-8a1d-9a0a444cc88c/GCA_017983755.1_ASM1798375v1_genomic.fna.gz --refList GCA_017983755.1_ASM1798375v1_genomic.fna/target_genomes.txt --output GCA_017983755.1_ASM1798375v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:35,640] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:35,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:35,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:35,648] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:35,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:31:35,648] [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
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	83.5967	569	819	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	83.4521	570	819	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	83.1	489	819	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	82.6874	455	819	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	79.2447	312	819	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.5154	244	819	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.0659	299	819	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	77.9072	296	819	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:31:35,649] [INFO] DFAST Taxonomy check result was written to GCA_017983755.1_ASM1798375v1_genomic.fna/tc_result.tsv
[2023-06-28 13:31:35,650] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:35,650] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:35,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/checkm_data
[2023-06-28 13:31:35,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:35,680] [INFO] Task started: CheckM
[2023-06-28 13:31:35,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017983755.1_ASM1798375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017983755.1_ASM1798375v1_genomic.fna/checkm_input GCA_017983755.1_ASM1798375v1_genomic.fna/checkm_result
[2023-06-28 13:31:57,918] [INFO] Task succeeded: CheckM
[2023-06-28 13:31:57,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:31:57,932] [INFO] ===== Completeness check finished =====
[2023-06-28 13:31:57,932] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:31:57,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017983755.1_ASM1798375v1_genomic.fna/markers.fasta)
[2023-06-28 13:31:57,933] [INFO] Task started: Blastn
[2023-06-28 13:31:57,933] [INFO] Running command: blastn -query GCA_017983755.1_ASM1798375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc3e6a07-354d-4128-959d-e55a47113837/dqc_reference/reference_markers_gtdb.fasta -out GCA_017983755.1_ASM1798375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:59,085] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:59,088] [INFO] Selected 12 target genomes.
[2023-06-28 13:31:59,088] [INFO] Target genome list was writen to GCA_017983755.1_ASM1798375v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:31:59,102] [INFO] Task started: fastANI
[2023-06-28 13:31:59,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b9b577a-441e-4001-8a1d-9a0a444cc88c/GCA_017983755.1_ASM1798375v1_genomic.fna.gz --refList GCA_017983755.1_ASM1798375v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017983755.1_ASM1798375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:08,461] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:08,469] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:32:08,469] [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
GCA_017983755.1	s__Azonexus sp017983755	100.0	817	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002440665.1	s__Azonexus sp002440665	89.5514	656	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	88.4416	695	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013363835.1	s__Azonexus sp013363835	86.0265	603	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790845.1	s__Azonexus sp016790845	85.4528	375	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469585.1	s__Azonexus sp009469585	83.9581	539	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302355.1	s__Azonexus sp017302355	83.7048	441	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001551835.1	s__Azonexus denitrificans	83.565	571	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983615.1	s__Azonexus sp017983615	83.3957	486	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	83.183	463	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	82.7306	545	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018261895.1	s__Azonexus sp018261895	82.5733	464	819	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:08,471] [INFO] GTDB search result was written to GCA_017983755.1_ASM1798375v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:08,471] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:08,474] [INFO] DFAST_QC result json was written to GCA_017983755.1_ASM1798375v1_genomic.fna/dqc_result.json
[2023-06-28 13:32:08,474] [INFO] DFAST_QC completed!
[2023-06-28 13:32:08,474] [INFO] Total running time: 0h0m47s