[2023-06-27 10:06:33,583] [INFO] DFAST_QC pipeline started.
[2023-06-27 10:06:33,666] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 10:06:33,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference
[2023-06-27 10:06:34,856] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 10:06:34,857] [INFO] Task started: Prodigal
[2023-06-27 10:06:34,857] [INFO] Running command: gunzip -c /var/lib/cwl/stgd88228cd-f456-476b-a659-09205d51c32c/GCA_002435335.1_ASM243533v1_genomic.fna.gz | prodigal -d GCA_002435335.1_ASM243533v1_genomic.fna/cds.fna -a GCA_002435335.1_ASM243533v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 10:06:40,740] [INFO] Task succeeded: Prodigal
[2023-06-27 10:06:40,740] [INFO] Task started: HMMsearch
[2023-06-27 10:06:40,740] [INFO] Running command: hmmsearch --tblout GCA_002435335.1_ASM243533v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/reference_markers.hmm GCA_002435335.1_ASM243533v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 10:06:40,968] [INFO] Task succeeded: HMMsearch
[2023-06-27 10:06:40,970] [INFO] Found 6/6 markers.
[2023-06-27 10:06:41,122] [INFO] Query marker FASTA was written to GCA_002435335.1_ASM243533v1_genomic.fna/markers.fasta
[2023-06-27 10:06:41,122] [INFO] Task started: Blastn
[2023-06-27 10:06:41,122] [INFO] Running command: blastn -query GCA_002435335.1_ASM243533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/reference_markers.fasta -out GCA_002435335.1_ASM243533v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:06:41,755] [INFO] Task succeeded: Blastn
[2023-06-27 10:06:41,761] [INFO] Selected 24 target genomes.
[2023-06-27 10:06:41,762] [INFO] Target genome list was writen to GCA_002435335.1_ASM243533v1_genomic.fna/target_genomes.txt
[2023-06-27 10:06:41,790] [INFO] Task started: fastANI
[2023-06-27 10:06:41,791] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88228cd-f456-476b-a659-09205d51c32c/GCA_002435335.1_ASM243533v1_genomic.fna.gz --refList GCA_002435335.1_ASM243533v1_genomic.fna/target_genomes.txt --output GCA_002435335.1_ASM243533v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 10:06:54,367] [INFO] Task succeeded: fastANI
[2023-06-27 10:06:54,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 10:06:54,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 10:06:54,379] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 10:06:54,379] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 10:06:54,379] [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	77.4558	202	659	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	76.711	108	659	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	76.4962	129	659	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	76.4741	127	659	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 10:06:54,465] [INFO] DFAST Taxonomy check result was written to GCA_002435335.1_ASM243533v1_genomic.fna/tc_result.tsv
[2023-06-27 10:06:54,466] [INFO] ===== Taxonomy check completed =====
[2023-06-27 10:06:54,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 10:06:54,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/checkm_data
[2023-06-27 10:06:54,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 10:06:54,510] [INFO] Task started: CheckM
[2023-06-27 10:06:54,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002435335.1_ASM243533v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002435335.1_ASM243533v1_genomic.fna/checkm_input GCA_002435335.1_ASM243533v1_genomic.fna/checkm_result
[2023-06-27 10:07:20,831] [INFO] Task succeeded: CheckM
[2023-06-27 10:07:20,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 10:07:20,891] [INFO] ===== Completeness check finished =====
[2023-06-27 10:07:20,892] [INFO] ===== Start GTDB Search =====
[2023-06-27 10:07:20,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002435335.1_ASM243533v1_genomic.fna/markers.fasta)
[2023-06-27 10:07:20,892] [INFO] Task started: Blastn
[2023-06-27 10:07:20,892] [INFO] Running command: blastn -query GCA_002435335.1_ASM243533v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0053ab40-aff3-4500-9b10-83cea0d79e59/dqc_reference/reference_markers_gtdb.fasta -out GCA_002435335.1_ASM243533v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 10:07:21,762] [INFO] Task succeeded: Blastn
[2023-06-27 10:07:21,782] [INFO] Selected 20 target genomes.
[2023-06-27 10:07:21,782] [INFO] Target genome list was writen to GCA_002435335.1_ASM243533v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 10:07:21,796] [INFO] Task started: fastANI
[2023-06-27 10:07:21,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88228cd-f456-476b-a659-09205d51c32c/GCA_002435335.1_ASM243533v1_genomic.fna.gz --refList GCA_002435335.1_ASM243533v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002435335.1_ASM243533v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 10:07:30,677] [INFO] Task succeeded: fastANI
[2023-06-27 10:07:30,688] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 10:07:30,688] [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_002435335.1	s__Nitrosomonas sp002435335	100.0	655	659	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_005779435.1	s__Nitrosomonas sp005779435	78.3045	232	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002083395.1	s__Nitrosomonas sp002083395	78.1172	179	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240935.1	s__Nitrosomonas sp018240935	77.6928	137	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709615.1	s__Nitrosomonas sp015709615	77.6659	206	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.12	98.12	0.95	0.95	2	-
GCF_004345375.1	s__Nitrosomonas sp004345375	77.6299	209	659	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	77.55	198	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.27	97.27	0.85	0.85	2	-
GCA_002083595.1	s__Nitrosomonas sp002083595	77.5109	190	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106555.1	s__Nitrosomonas oligotropha_A	77.5004	208	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.13	95.07	0.88	0.80	7	-
GCF_009833085.1	s__Nitrosomonas oligotropha	77.4712	201	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.57	96.57	0.86	0.86	2	-
GCA_018241205.1	s__Nitrosomonas sp018241205	77.2781	149	659	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	76.7286	136	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017984435.1	s__Nitrosomonas sp017984435	76.5027	119	659	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-27 10:07:30,707] [INFO] GTDB search result was written to GCA_002435335.1_ASM243533v1_genomic.fna/result_gtdb.tsv
[2023-06-27 10:07:30,708] [INFO] ===== GTDB Search completed =====
[2023-06-27 10:07:30,713] [INFO] DFAST_QC result json was written to GCA_002435335.1_ASM243533v1_genomic.fna/dqc_result.json
[2023-06-27 10:07:30,713] [INFO] DFAST_QC completed!
[2023-06-27 10:07:30,713] [INFO] Total running time: 0h0m57s