[2023-06-19 01:46:29,399] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:46:29,401] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:46:29,401] [INFO] DQC Reference Directory: /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference
[2023-06-19 01:46:30,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:46:30,593] [INFO] Task started: Prodigal
[2023-06-19 01:46:30,594] [INFO] Running command: gunzip -c /var/lib/cwl/stga3e16ccf-9376-400c-9a88-0ced1bd36933/GCA_018053985.1_ASM1805398v1_genomic.fna.gz | prodigal -d GCA_018053985.1_ASM1805398v1_genomic.fna/cds.fna -a GCA_018053985.1_ASM1805398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:46:33,847] [INFO] Task succeeded: Prodigal
[2023-06-19 01:46:33,847] [INFO] Task started: HMMsearch
[2023-06-19 01:46:33,848] [INFO] Running command: hmmsearch --tblout GCA_018053985.1_ASM1805398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/reference_markers.hmm GCA_018053985.1_ASM1805398v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:46:34,010] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:46:34,011] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga3e16ccf-9376-400c-9a88-0ced1bd36933/GCA_018053985.1_ASM1805398v1_genomic.fna.gz]
[2023-06-19 01:46:34,027] [INFO] Query marker FASTA was written to GCA_018053985.1_ASM1805398v1_genomic.fna/markers.fasta
[2023-06-19 01:46:34,027] [INFO] Task started: Blastn
[2023-06-19 01:46:34,027] [INFO] Running command: blastn -query GCA_018053985.1_ASM1805398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/reference_markers.fasta -out GCA_018053985.1_ASM1805398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:46:34,655] [INFO] Task succeeded: Blastn
[2023-06-19 01:46:34,660] [INFO] Selected 14 target genomes.
[2023-06-19 01:46:34,660] [INFO] Target genome list was writen to GCA_018053985.1_ASM1805398v1_genomic.fna/target_genomes.txt
[2023-06-19 01:46:34,662] [INFO] Task started: fastANI
[2023-06-19 01:46:34,662] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e16ccf-9376-400c-9a88-0ced1bd36933/GCA_018053985.1_ASM1805398v1_genomic.fna.gz --refList GCA_018053985.1_ASM1805398v1_genomic.fna/target_genomes.txt --output GCA_018053985.1_ASM1805398v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:46:43,062] [INFO] Task succeeded: fastANI
[2023-06-19 01:46:43,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:46:43,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:46:43,074] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:46:43,074] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 01:46:43,075] [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
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.1928	161	260	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	79.8719	142	260	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	79.8438	141	260	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	79.6882	153	260	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	79.5818	148	260	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	79.5304	143	260	95	below_threshold
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	79.3648	151	260	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.2752	157	260	95	below_threshold
Comamonas kerstersii	strain=CCUG 15333	GCA_008801935.1	225992	225992	type	True	79.0377	156	260	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	78.9847	143	260	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	78.7789	136	260	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	78.6703	131	260	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	78.6314	100	260	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.4755	130	260	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 01:46:43,076] [INFO] DFAST Taxonomy check result was written to GCA_018053985.1_ASM1805398v1_genomic.fna/tc_result.tsv
[2023-06-19 01:46:43,077] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:46:43,077] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:46:43,077] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/checkm_data
[2023-06-19 01:46:43,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:46:43,093] [INFO] Task started: CheckM
[2023-06-19 01:46:43,093] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018053985.1_ASM1805398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018053985.1_ASM1805398v1_genomic.fna/checkm_input GCA_018053985.1_ASM1805398v1_genomic.fna/checkm_result
[2023-06-19 01:46:59,108] [INFO] Task succeeded: CheckM
[2023-06-19 01:46:59,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 01:46:59,132] [INFO] ===== Completeness check finished =====
[2023-06-19 01:46:59,132] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:46:59,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018053985.1_ASM1805398v1_genomic.fna/markers.fasta)
[2023-06-19 01:46:59,133] [INFO] Task started: Blastn
[2023-06-19 01:46:59,133] [INFO] Running command: blastn -query GCA_018053985.1_ASM1805398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc38b9970-30b8-4b92-b087-e8def3bc63ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_018053985.1_ASM1805398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:47:00,100] [INFO] Task succeeded: Blastn
[2023-06-19 01:47:00,104] [INFO] Selected 9 target genomes.
[2023-06-19 01:47:00,104] [INFO] Target genome list was writen to GCA_018053985.1_ASM1805398v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:47:00,109] [INFO] Task started: fastANI
[2023-06-19 01:47:00,109] [INFO] Running command: fastANI --query /var/lib/cwl/stga3e16ccf-9376-400c-9a88-0ced1bd36933/GCA_018053985.1_ASM1805398v1_genomic.fna.gz --refList GCA_018053985.1_ASM1805398v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018053985.1_ASM1805398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:47:05,346] [INFO] Task succeeded: fastANI
[2023-06-19 01:47:05,356] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:47:05,356] [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_017368815.1	s__Comamonas denitrificans_A	98.4801	255	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.17	97.65	0.93	0.87	4	conclusive
GCA_019104825.1	s__Comamonas sp019104825	83.49	178	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739875.1	s__Comamonas aquatica	80.1928	161	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCA_001725235.1	s__Acidovorax_C sp001725235	79.8719	149	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
GCF_011303755.1	s__Acidovorax_C sp011303755	79.8493	169	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637085.1	s__Comamonas phosphati	79.3953	150	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001544075.1	s__Comamonas terrae	79.2752	157	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019186805.1	s__Comamonas sp019186805	79.0169	142	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	78.8762	117	260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:47:05,359] [INFO] GTDB search result was written to GCA_018053985.1_ASM1805398v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:47:05,359] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:47:05,363] [INFO] DFAST_QC result json was written to GCA_018053985.1_ASM1805398v1_genomic.fna/dqc_result.json
[2023-06-19 01:47:05,363] [INFO] DFAST_QC completed!
[2023-06-19 01:47:05,363] [INFO] Total running time: 0h0m36s