[2023-06-29 23:16:23,971] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:16:23,973] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:16:23,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference
[2023-06-29 23:16:25,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:16:25,271] [INFO] Task started: Prodigal
[2023-06-29 23:16:25,272] [INFO] Running command: gunzip -c /var/lib/cwl/stg20ca957e-4700-43cf-9819-b4572526665c/GCA_008015565.1_ASM801556v1_genomic.fna.gz | prodigal -d GCA_008015565.1_ASM801556v1_genomic.fna/cds.fna -a GCA_008015565.1_ASM801556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:16:31,333] [INFO] Task succeeded: Prodigal
[2023-06-29 23:16:31,333] [INFO] Task started: HMMsearch
[2023-06-29 23:16:31,333] [INFO] Running command: hmmsearch --tblout GCA_008015565.1_ASM801556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/reference_markers.hmm GCA_008015565.1_ASM801556v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:16:31,568] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:16:31,570] [INFO] Found 6/6 markers.
[2023-06-29 23:16:31,600] [INFO] Query marker FASTA was written to GCA_008015565.1_ASM801556v1_genomic.fna/markers.fasta
[2023-06-29 23:16:31,601] [INFO] Task started: Blastn
[2023-06-29 23:16:31,601] [INFO] Running command: blastn -query GCA_008015565.1_ASM801556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/reference_markers.fasta -out GCA_008015565.1_ASM801556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:16:32,215] [INFO] Task succeeded: Blastn
[2023-06-29 23:16:32,220] [INFO] Selected 23 target genomes.
[2023-06-29 23:16:32,220] [INFO] Target genome list was writen to GCA_008015565.1_ASM801556v1_genomic.fna/target_genomes.txt
[2023-06-29 23:16:32,225] [INFO] Task started: fastANI
[2023-06-29 23:16:32,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ca957e-4700-43cf-9819-b4572526665c/GCA_008015565.1_ASM801556v1_genomic.fna.gz --refList GCA_008015565.1_ASM801556v1_genomic.fna/target_genomes.txt --output GCA_008015565.1_ASM801556v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:16:42,946] [INFO] Task succeeded: fastANI
[2023-06-29 23:16:42,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:16:42,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:16:42,956] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:16:42,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:16:42,956] [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 ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	77.0921	173	798	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	77.0897	178	798	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	76.7969	150	798	95	below_threshold
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	76.7849	176	798	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:16:42,959] [INFO] DFAST Taxonomy check result was written to GCA_008015565.1_ASM801556v1_genomic.fna/tc_result.tsv
[2023-06-29 23:16:42,960] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:16:42,960] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:16:42,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/checkm_data
[2023-06-29 23:16:42,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:16:42,989] [INFO] Task started: CheckM
[2023-06-29 23:16:42,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_008015565.1_ASM801556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_008015565.1_ASM801556v1_genomic.fna/checkm_input GCA_008015565.1_ASM801556v1_genomic.fna/checkm_result
[2023-06-29 23:17:07,492] [INFO] Task succeeded: CheckM
[2023-06-29 23:17:07,494] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:17:07,516] [INFO] ===== Completeness check finished =====
[2023-06-29 23:17:07,517] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:17:07,517] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_008015565.1_ASM801556v1_genomic.fna/markers.fasta)
[2023-06-29 23:17:07,518] [INFO] Task started: Blastn
[2023-06-29 23:17:07,518] [INFO] Running command: blastn -query GCA_008015565.1_ASM801556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0990c703-fabe-4f66-8778-c744b6fb7599/dqc_reference/reference_markers_gtdb.fasta -out GCA_008015565.1_ASM801556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:17:08,324] [INFO] Task succeeded: Blastn
[2023-06-29 23:17:08,328] [INFO] Selected 14 target genomes.
[2023-06-29 23:17:08,328] [INFO] Target genome list was writen to GCA_008015565.1_ASM801556v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:17:08,341] [INFO] Task started: fastANI
[2023-06-29 23:17:08,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ca957e-4700-43cf-9819-b4572526665c/GCA_008015565.1_ASM801556v1_genomic.fna.gz --refList GCA_008015565.1_ASM801556v1_genomic.fna/target_genomes_gtdb.txt --output GCA_008015565.1_ASM801556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:17:15,926] [INFO] Task succeeded: fastANI
[2023-06-29 23:17:15,940] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:17:15,940] [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_008015565.1	s__Nitrosomonas sp008015565	100.0	794	798	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_900696615.1	s__Nitrosomonas sp900696615	90.32	626	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826055.1	s__Nitrosomonas sp902826055	82.8307	546	798	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	77.4802	261	798	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	77.443	226	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.98	99.98	0.97	0.97	2	-
GCF_900106555.1	s__Nitrosomonas oligotropha_A	77.3979	181	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.13	95.07	0.88	0.80	7	-
GCF_900108305.1	s__Nitrosomonas ureae_B	77.2798	162	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112825.1	s__Nitrosomonas sp900112825	77.1677	231	798	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	77.0822	212	798	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	77.0179	180	798	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	96.06	96.06	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:17:15,942] [INFO] GTDB search result was written to GCA_008015565.1_ASM801556v1_genomic.fna/result_gtdb.tsv
[2023-06-29 23:17:15,943] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:17:15,946] [INFO] DFAST_QC result json was written to GCA_008015565.1_ASM801556v1_genomic.fna/dqc_result.json
[2023-06-29 23:17:15,946] [INFO] DFAST_QC completed!
[2023-06-29 23:17:15,946] [INFO] Total running time: 0h0m52s