[2023-06-30 20:19:37,288] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:19:37,291] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:19:37,291] [INFO] DQC Reference Directory: /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference
[2023-06-30 20:19:38,667] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:19:38,668] [INFO] Task started: Prodigal
[2023-06-30 20:19:38,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ba69a2c-67c4-49b9-8008-e8eb705e21ba/GCA_016708955.1_ASM1670895v1_genomic.fna.gz | prodigal -d GCA_016708955.1_ASM1670895v1_genomic.fna/cds.fna -a GCA_016708955.1_ASM1670895v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:19:47,744] [INFO] Task succeeded: Prodigal
[2023-06-30 20:19:47,744] [INFO] Task started: HMMsearch
[2023-06-30 20:19:47,744] [INFO] Running command: hmmsearch --tblout GCA_016708955.1_ASM1670895v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/reference_markers.hmm GCA_016708955.1_ASM1670895v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:19:48,027] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:19:48,028] [INFO] Found 6/6 markers.
[2023-06-30 20:19:48,059] [INFO] Query marker FASTA was written to GCA_016708955.1_ASM1670895v1_genomic.fna/markers.fasta
[2023-06-30 20:19:48,059] [INFO] Task started: Blastn
[2023-06-30 20:19:48,059] [INFO] Running command: blastn -query GCA_016708955.1_ASM1670895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/reference_markers.fasta -out GCA_016708955.1_ASM1670895v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:19:48,744] [INFO] Task succeeded: Blastn
[2023-06-30 20:19:48,747] [INFO] Selected 32 target genomes.
[2023-06-30 20:19:48,748] [INFO] Target genome list was writen to GCA_016708955.1_ASM1670895v1_genomic.fna/target_genomes.txt
[2023-06-30 20:19:48,754] [INFO] Task started: fastANI
[2023-06-30 20:19:48,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ba69a2c-67c4-49b9-8008-e8eb705e21ba/GCA_016708955.1_ASM1670895v1_genomic.fna.gz --refList GCA_016708955.1_ASM1670895v1_genomic.fna/target_genomes.txt --output GCA_016708955.1_ASM1670895v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:20:06,581] [INFO] Task succeeded: fastANI
[2023-06-30 20:20:06,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:20:06,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:20:06,589] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:20:06,589] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:20:06,589] [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
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	79.0918	385	1134	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	78.7015	335	1134	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	78.5952	327	1134	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	78.2005	328	1134	95	below_threshold
Nitrosomonas communis	strain=Nm2	GCA_008124795.1	44574	44574	type	True	77.3162	67	1134	95	below_threshold
Nitrosomonas communis	strain=Nm2	GCA_001007935.1	44574	44574	type	True	77.2944	67	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:20:06,592] [INFO] DFAST Taxonomy check result was written to GCA_016708955.1_ASM1670895v1_genomic.fna/tc_result.tsv
[2023-06-30 20:20:06,592] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:20:06,592] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:20:06,592] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/checkm_data
[2023-06-30 20:20:06,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:20:06,636] [INFO] Task started: CheckM
[2023-06-30 20:20:06,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708955.1_ASM1670895v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708955.1_ASM1670895v1_genomic.fna/checkm_input GCA_016708955.1_ASM1670895v1_genomic.fna/checkm_result
[2023-06-30 20:20:38,963] [INFO] Task succeeded: CheckM
[2023-06-30 20:20:38,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:20:38,986] [INFO] ===== Completeness check finished =====
[2023-06-30 20:20:38,987] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:20:38,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708955.1_ASM1670895v1_genomic.fna/markers.fasta)
[2023-06-30 20:20:38,987] [INFO] Task started: Blastn
[2023-06-30 20:20:38,988] [INFO] Running command: blastn -query GCA_016708955.1_ASM1670895v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg931b921f-d13f-4988-b434-2d80933b98f5/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708955.1_ASM1670895v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:20:40,043] [INFO] Task succeeded: Blastn
[2023-06-30 20:20:40,047] [INFO] Selected 14 target genomes.
[2023-06-30 20:20:40,047] [INFO] Target genome list was writen to GCA_016708955.1_ASM1670895v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:20:40,104] [INFO] Task started: fastANI
[2023-06-30 20:20:40,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ba69a2c-67c4-49b9-8008-e8eb705e21ba/GCA_016708955.1_ASM1670895v1_genomic.fna.gz --refList GCA_016708955.1_ASM1670895v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708955.1_ASM1670895v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:20:52,361] [INFO] Task succeeded: fastANI
[2023-06-30 20:20:52,380] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:20:52,380] [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_016708955.1	s__Nitrosomonas sp016708955	100.0	1133	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000219585.1	s__Nitrosomonas sp000219585	89.2648	801	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721865.1	s__Nitrosomonas sp016721865	87.5377	654	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984435.1	s__Nitrosomonas sp017984435	79.9456	462	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.98	99.98	0.97	0.97	2	-
GCF_003201565.1	s__Nitrosomonas sp003201565	79.7437	462	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900106555.1	s__Nitrosomonas oligotropha_A	79.382	379	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.13	95.07	0.88	0.80	7	-
GCF_004345375.1	s__Nitrosomonas sp004345375	78.9702	381	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083595.1	s__Nitrosomonas sp002083595	78.9492	352	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826915.1	s__Nitrosomonas sp902826915	78.9343	300	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108305.1	s__Nitrosomonas ureae_B	78.8496	330	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826115.1	s__Nitrosomonas sp902826115	78.7185	370	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.11	98.94	0.89	0.89	3	-
GCA_018241205.1	s__Nitrosomonas sp018241205	78.6549	285	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011925.2	s__Nitrosomonas sp003011925	78.21	327	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001007935.1	s__Nitrosomonas communis	77.3321	67	1134	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.46	96.92	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2023-06-30 20:20:52,382] [INFO] GTDB search result was written to GCA_016708955.1_ASM1670895v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:20:52,383] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:20:52,386] [INFO] DFAST_QC result json was written to GCA_016708955.1_ASM1670895v1_genomic.fna/dqc_result.json
[2023-06-30 20:20:52,386] [INFO] DFAST_QC completed!
[2023-06-30 20:20:52,386] [INFO] Total running time: 0h1m15s