[2024-01-24 13:32:41,112] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference
[2024-01-24 13:32:42,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,385] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg89853c9e-caca-448d-bb7e-937ada85fe9e/GCF_003011925.2_ASM301192v2_genomic.fna.gz | prodigal -d GCF_003011925.2_ASM301192v2_genomic.fna/cds.fna -a GCF_003011925.2_ASM301192v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:50,230] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:50,230] [INFO] Task started: HMMsearch
[2024-01-24 13:32:50,230] [INFO] Running command: hmmsearch --tblout GCF_003011925.2_ASM301192v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/reference_markers.hmm GCF_003011925.2_ASM301192v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:50,552] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:50,553] [INFO] Found 6/6 markers.
[2024-01-24 13:32:50,591] [INFO] Query marker FASTA was written to GCF_003011925.2_ASM301192v2_genomic.fna/markers.fasta
[2024-01-24 13:32:50,592] [INFO] Task started: Blastn
[2024-01-24 13:32:50,592] [INFO] Running command: blastn -query GCF_003011925.2_ASM301192v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/reference_markers.fasta -out GCF_003011925.2_ASM301192v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:51,201] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:51,205] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:51,205] [INFO] Target genome list was writen to GCF_003011925.2_ASM301192v2_genomic.fna/target_genomes.txt
[2024-01-24 13:32:51,224] [INFO] Task started: fastANI
[2024-01-24 13:32:51,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg89853c9e-caca-448d-bb7e-937ada85fe9e/GCF_003011925.2_ASM301192v2_genomic.fna.gz --refList GCF_003011925.2_ASM301192v2_genomic.fna/target_genomes.txt --output GCF_003011925.2_ASM301192v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:00,340] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:00,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:00,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:00,346] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:00,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:00,347] [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 supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	100.0	1147	1152	95	conclusive
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	81.6719	691	1152	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	81.6298	708	1152	95	below_threshold
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	77.7743	249	1152	95	below_threshold
Nitrosomonas marina	strain=Nm22	GCA_900110145.1	917	917	type	True	76.6881	67	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:00,348] [INFO] DFAST Taxonomy check result was written to GCF_003011925.2_ASM301192v2_genomic.fna/tc_result.tsv
[2024-01-24 13:33:00,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:00,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:00,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/checkm_data
[2024-01-24 13:33:00,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:00,401] [INFO] Task started: CheckM
[2024-01-24 13:33:00,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003011925.2_ASM301192v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003011925.2_ASM301192v2_genomic.fna/checkm_input GCF_003011925.2_ASM301192v2_genomic.fna/checkm_result
[2024-01-24 13:33:28,429] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:28,430] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:28,447] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:28,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:28,447] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003011925.2_ASM301192v2_genomic.fna/markers.fasta)
[2024-01-24 13:33:28,448] [INFO] Task started: Blastn
[2024-01-24 13:33:28,448] [INFO] Running command: blastn -query GCF_003011925.2_ASM301192v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9af030dd-42ea-4de2-8bff-b97ab4114824/dqc_reference/reference_markers_gtdb.fasta -out GCF_003011925.2_ASM301192v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:29,456] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:29,459] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:29,459] [INFO] Target genome list was writen to GCF_003011925.2_ASM301192v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:29,465] [INFO] Task started: fastANI
[2024-01-24 13:33:29,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg89853c9e-caca-448d-bb7e-937ada85fe9e/GCF_003011925.2_ASM301192v2_genomic.fna.gz --refList GCF_003011925.2_ASM301192v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003011925.2_ASM301192v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:37,242] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:37,248] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:37,248] [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_003011925.2	s__Nitrosomonas sp003011925	100.0	1147	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902826915.1	s__Nitrosomonas sp902826915	83.4639	649	1152	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	81.7707	679	1152	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	81.6336	709	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.53	97.95	0.91	0.88	6	-
GCF_000175095.2	s__Nitrosomonas sp000175095	81.4346	689	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.06	96.06	0.86	0.86	2	-
GCA_016708955.1	s__Nitrosomonas sp016708955	77.9189	333	1152	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	77.8975	243	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.11	98.94	0.89	0.89	3	-
GCF_000219585.1	s__Nitrosomonas sp000219585	77.8923	372	1152	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	77.2349	68	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.46	96.92	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:37,250] [INFO] GTDB search result was written to GCF_003011925.2_ASM301192v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:37,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:37,252] [INFO] DFAST_QC result json was written to GCF_003011925.2_ASM301192v2_genomic.fna/dqc_result.json
[2024-01-24 13:33:37,252] [INFO] DFAST_QC completed!
[2024-01-24 13:33:37,253] [INFO] Total running time: 0h0m56s