[2023-06-28 13:05:35,383] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:05:35,387] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:05:35,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference
[2023-06-28 13:05:36,612] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:05:36,613] [INFO] Task started: Prodigal
[2023-06-28 13:05:36,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg478996d9-3508-4188-94f6-9c846e50c802/GCA_020446105.1_ASM2044610v1_genomic.fna.gz | prodigal -d GCA_020446105.1_ASM2044610v1_genomic.fna/cds.fna -a GCA_020446105.1_ASM2044610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:05:42,029] [INFO] Task succeeded: Prodigal
[2023-06-28 13:05:42,029] [INFO] Task started: HMMsearch
[2023-06-28 13:05:42,029] [INFO] Running command: hmmsearch --tblout GCA_020446105.1_ASM2044610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/reference_markers.hmm GCA_020446105.1_ASM2044610v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:05:42,289] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:05:42,291] [INFO] Found 6/6 markers.
[2023-06-28 13:05:42,317] [INFO] Query marker FASTA was written to GCA_020446105.1_ASM2044610v1_genomic.fna/markers.fasta
[2023-06-28 13:05:42,317] [INFO] Task started: Blastn
[2023-06-28 13:05:42,317] [INFO] Running command: blastn -query GCA_020446105.1_ASM2044610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/reference_markers.fasta -out GCA_020446105.1_ASM2044610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:05:42,938] [INFO] Task succeeded: Blastn
[2023-06-28 13:05:42,942] [INFO] Selected 29 target genomes.
[2023-06-28 13:05:42,943] [INFO] Target genome list was writen to GCA_020446105.1_ASM2044610v1_genomic.fna/target_genomes.txt
[2023-06-28 13:05:42,951] [INFO] Task started: fastANI
[2023-06-28 13:05:42,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg478996d9-3508-4188-94f6-9c846e50c802/GCA_020446105.1_ASM2044610v1_genomic.fna.gz --refList GCA_020446105.1_ASM2044610v1_genomic.fna/target_genomes.txt --output GCA_020446105.1_ASM2044610v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:06:02,604] [INFO] Task succeeded: fastANI
[2023-06-28 13:06:02,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:06:02,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:06:02,609] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:06:02,609] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:06:02,609] [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 aestuarii	strain=Nm36	GCA_003046585.1	52441	52441	type	True	76.8081	109	544	95	below_threshold
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	76.7847	63	544	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:06:02,612] [INFO] DFAST Taxonomy check result was written to GCA_020446105.1_ASM2044610v1_genomic.fna/tc_result.tsv
[2023-06-28 13:06:02,613] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:06:02,614] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:06:02,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/checkm_data
[2023-06-28 13:06:02,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:06:02,649] [INFO] Task started: CheckM
[2023-06-28 13:06:02,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020446105.1_ASM2044610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020446105.1_ASM2044610v1_genomic.fna/checkm_input GCA_020446105.1_ASM2044610v1_genomic.fna/checkm_result
[2023-06-28 13:06:25,685] [INFO] Task succeeded: CheckM
[2023-06-28 13:06:25,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:06:25,708] [INFO] ===== Completeness check finished =====
[2023-06-28 13:06:25,708] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:06:25,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020446105.1_ASM2044610v1_genomic.fna/markers.fasta)
[2023-06-28 13:06:25,709] [INFO] Task started: Blastn
[2023-06-28 13:06:25,709] [INFO] Running command: blastn -query GCA_020446105.1_ASM2044610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg289bed78-cbf2-4346-aca3-a49c3f9e7647/dqc_reference/reference_markers_gtdb.fasta -out GCA_020446105.1_ASM2044610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:06:26,541] [INFO] Task succeeded: Blastn
[2023-06-28 13:06:26,546] [INFO] Selected 27 target genomes.
[2023-06-28 13:06:26,546] [INFO] Target genome list was writen to GCA_020446105.1_ASM2044610v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:06:26,560] [INFO] Task started: fastANI
[2023-06-28 13:06:26,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg478996d9-3508-4188-94f6-9c846e50c802/GCA_020446105.1_ASM2044610v1_genomic.fna.gz --refList GCA_020446105.1_ASM2044610v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020446105.1_ASM2044610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:06:39,394] [INFO] Task succeeded: fastANI
[2023-06-28 13:06:39,409] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 13:06:39,409] [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_003046585.1	s__Nitrosomonas aestuarii	76.7863	110	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.25	97.25	0.92	0.92	2	-
GCF_009833085.1	s__Nitrosomonas oligotropha	76.7847	63	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.57	96.57	0.86	0.86	2	-
GCA_017984435.1	s__Nitrosomonas sp017984435	76.7786	59	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.98	99.98	0.97	0.97	2	-
GCF_900108305.1	s__Nitrosomonas ureae_B	76.6256	62	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003514765.1	s__Nitrosomonas sp003514765	76.5509	67	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345375.1	s__Nitrosomonas sp004345375	76.5151	59	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240285.1	s__Nitrosomonas sp018240285	76.2595	73	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.27	97.27	0.85	0.85	2	-
GCF_000219585.1	s__Nitrosomonas sp000219585	76.233	54	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201565.1	s__Nitrosomonas sp003201565	76.1407	57	544	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-28 13:06:39,411] [INFO] GTDB search result was written to GCA_020446105.1_ASM2044610v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:06:39,412] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:06:39,415] [INFO] DFAST_QC result json was written to GCA_020446105.1_ASM2044610v1_genomic.fna/dqc_result.json
[2023-06-28 13:06:39,415] [INFO] DFAST_QC completed!
[2023-06-28 13:06:39,415] [INFO] Total running time: 0h1m4s