[2023-06-28 07:56:55,394] [INFO] DFAST_QC pipeline started.
[2023-06-28 07:56:55,397] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 07:56:55,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference
[2023-06-28 07:56:56,810] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 07:56:56,811] [INFO] Task started: Prodigal
[2023-06-28 07:56:56,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg77f6fecf-032d-4b60-adf7-dadf38181dfa/GCA_019635155.1_ASM1963515v1_genomic.fna.gz | prodigal -d GCA_019635155.1_ASM1963515v1_genomic.fna/cds.fna -a GCA_019635155.1_ASM1963515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 07:57:05,552] [INFO] Task succeeded: Prodigal
[2023-06-28 07:57:05,553] [INFO] Task started: HMMsearch
[2023-06-28 07:57:05,553] [INFO] Running command: hmmsearch --tblout GCA_019635155.1_ASM1963515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/reference_markers.hmm GCA_019635155.1_ASM1963515v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 07:57:05,813] [INFO] Task succeeded: HMMsearch
[2023-06-28 07:57:05,814] [INFO] Found 6/6 markers.
[2023-06-28 07:57:05,846] [INFO] Query marker FASTA was written to GCA_019635155.1_ASM1963515v1_genomic.fna/markers.fasta
[2023-06-28 07:57:05,847] [INFO] Task started: Blastn
[2023-06-28 07:57:05,847] [INFO] Running command: blastn -query GCA_019635155.1_ASM1963515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/reference_markers.fasta -out GCA_019635155.1_ASM1963515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:06,482] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:06,486] [INFO] Selected 19 target genomes.
[2023-06-28 07:57:06,486] [INFO] Target genome list was writen to GCA_019635155.1_ASM1963515v1_genomic.fna/target_genomes.txt
[2023-06-28 07:57:06,511] [INFO] Task started: fastANI
[2023-06-28 07:57:06,511] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f6fecf-032d-4b60-adf7-dadf38181dfa/GCA_019635155.1_ASM1963515v1_genomic.fna.gz --refList GCA_019635155.1_ASM1963515v1_genomic.fna/target_genomes.txt --output GCA_019635155.1_ASM1963515v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 07:57:17,325] [INFO] Task succeeded: fastANI
[2023-06-28 07:57:17,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 07:57:17,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 07:57:17,333] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 07:57:17,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 07:57:17,333] [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	78.8381	339	1005	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	78.2291	234	1005	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	78.205	241	1005	95	below_threshold
Nitrosomonas marina	strain=Nm22	GCA_900110145.1	917	917	type	True	76.8588	59	1005	95	below_threshold
Nitrosomonas aestuarii	strain=Nm36	GCA_003046585.1	52441	52441	type	True	76.5883	79	1005	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 07:57:17,336] [INFO] DFAST Taxonomy check result was written to GCA_019635155.1_ASM1963515v1_genomic.fna/tc_result.tsv
[2023-06-28 07:57:17,336] [INFO] ===== Taxonomy check completed =====
[2023-06-28 07:57:17,336] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 07:57:17,337] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/checkm_data
[2023-06-28 07:57:17,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 07:57:17,373] [INFO] Task started: CheckM
[2023-06-28 07:57:17,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019635155.1_ASM1963515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019635155.1_ASM1963515v1_genomic.fna/checkm_input GCA_019635155.1_ASM1963515v1_genomic.fna/checkm_result
[2023-06-28 07:57:48,614] [INFO] Task succeeded: CheckM
[2023-06-28 07:57:48,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 07:57:48,636] [INFO] ===== Completeness check finished =====
[2023-06-28 07:57:48,636] [INFO] ===== Start GTDB Search =====
[2023-06-28 07:57:48,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019635155.1_ASM1963515v1_genomic.fna/markers.fasta)
[2023-06-28 07:57:48,637] [INFO] Task started: Blastn
[2023-06-28 07:57:48,637] [INFO] Running command: blastn -query GCA_019635155.1_ASM1963515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d5cc391-a306-4749-8b80-8c0382dae177/dqc_reference/reference_markers_gtdb.fasta -out GCA_019635155.1_ASM1963515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 07:57:49,525] [INFO] Task succeeded: Blastn
[2023-06-28 07:57:49,530] [INFO] Selected 17 target genomes.
[2023-06-28 07:57:49,530] [INFO] Target genome list was writen to GCA_019635155.1_ASM1963515v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 07:57:49,581] [INFO] Task started: fastANI
[2023-06-28 07:57:49,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f6fecf-032d-4b60-adf7-dadf38181dfa/GCA_019635155.1_ASM1963515v1_genomic.fna.gz --refList GCA_019635155.1_ASM1963515v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019635155.1_ASM1963515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 07:57:58,651] [INFO] Task succeeded: fastANI
[2023-06-28 07:57:58,663] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 07:57:58,663] [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_002083395.1	s__Nitrosomonas sp002083395	82.6397	665	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709635.1	s__Nitrosomonas sp015709635	79.3714	362	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	95.39	95.39	0.89	0.89	2	-
GCA_015709615.1	s__Nitrosomonas sp015709615	79.3649	369	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.12	98.12	0.95	0.95	2	-
GCA_018240285.1	s__Nitrosomonas sp018240285	79.0762	323	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.27	97.27	0.85	0.85	2	-
GCF_004345375.1	s__Nitrosomonas sp004345375	78.9715	366	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833085.1	s__Nitrosomonas oligotropha	78.8511	338	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.57	96.57	0.86	0.86	2	-
GCA_002083595.1	s__Nitrosomonas sp002083595	78.7699	320	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241205.1	s__Nitrosomonas sp018241205	78.6501	294	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175095.2	s__Nitrosomonas sp000175095	78.6488	227	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.06	96.06	0.86	0.86	2	-
GCA_018240935.1	s__Nitrosomonas sp018240935	78.5447	217	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455205.1	s__Nitrosomonas ureae	78.2391	240	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.53	97.95	0.91	0.88	6	-
GCA_902826055.1	s__Nitrosomonas sp902826055	77.8755	175	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219585.1	s__Nitrosomonas sp000219585	77.6311	261	1005	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	77.247	183	1005	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.11	98.94	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-28 07:57:58,665] [INFO] GTDB search result was written to GCA_019635155.1_ASM1963515v1_genomic.fna/result_gtdb.tsv
[2023-06-28 07:57:58,666] [INFO] ===== GTDB Search completed =====
[2023-06-28 07:57:58,670] [INFO] DFAST_QC result json was written to GCA_019635155.1_ASM1963515v1_genomic.fna/dqc_result.json
[2023-06-28 07:57:58,670] [INFO] DFAST_QC completed!
[2023-06-28 07:57:58,670] [INFO] Total running time: 0h1m3s