[2023-06-28 17:29:48,093] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:29:48,096] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:29:48,096] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference
[2023-06-28 17:29:49,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:29:49,500] [INFO] Task started: Prodigal
[2023-06-28 17:29:49,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b5a6dea-7da4-4a7f-9ec0-9aa9876c00af/GCA_020852475.1_ASM2085247v1_genomic.fna.gz | prodigal -d GCA_020852475.1_ASM2085247v1_genomic.fna/cds.fna -a GCA_020852475.1_ASM2085247v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:29:56,584] [INFO] Task succeeded: Prodigal
[2023-06-28 17:29:56,584] [INFO] Task started: HMMsearch
[2023-06-28 17:29:56,584] [INFO] Running command: hmmsearch --tblout GCA_020852475.1_ASM2085247v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/reference_markers.hmm GCA_020852475.1_ASM2085247v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:29:56,777] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:29:56,778] [INFO] Found 6/6 markers.
[2023-06-28 17:29:56,804] [INFO] Query marker FASTA was written to GCA_020852475.1_ASM2085247v1_genomic.fna/markers.fasta
[2023-06-28 17:29:56,805] [INFO] Task started: Blastn
[2023-06-28 17:29:56,805] [INFO] Running command: blastn -query GCA_020852475.1_ASM2085247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/reference_markers.fasta -out GCA_020852475.1_ASM2085247v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:29:57,429] [INFO] Task succeeded: Blastn
[2023-06-28 17:29:57,434] [INFO] Selected 24 target genomes.
[2023-06-28 17:29:57,434] [INFO] Target genome list was writen to GCA_020852475.1_ASM2085247v1_genomic.fna/target_genomes.txt
[2023-06-28 17:29:57,440] [INFO] Task started: fastANI
[2023-06-28 17:29:57,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5a6dea-7da4-4a7f-9ec0-9aa9876c00af/GCA_020852475.1_ASM2085247v1_genomic.fna.gz --refList GCA_020852475.1_ASM2085247v1_genomic.fna/target_genomes.txt --output GCA_020852475.1_ASM2085247v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:30:10,632] [INFO] Task succeeded: fastANI
[2023-06-28 17:30:10,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:30:10,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:30:10,640] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:30:10,640] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:30:10,640] [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 nitrosa	strain=Nm90	GCA_003051105.1	52442	52442	type	True	77.9079	58	881	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_001455205.1	44577	44577	type	True	77.305	70	881	95	below_threshold
Nitrosomonas oligotropha	strain=Nm45	GCA_009833085.1	42354	42354	type	True	77.2118	126	881	95	below_threshold
Nitrosomonas ureae	strain=Nm10	GCA_900105875.1	44577	44577	type	True	77.1582	69	881	95	below_threshold
Nitrosomonas supralitoralis	strain=APG5	GCA_003011925.2	2116706	2116706	type	True	77.0317	62	881	95	below_threshold
Nitrosomonas aestuarii	strain=Nm36	GCA_003046585.1	52441	52441	type	True	76.5544	154	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:30:10,642] [INFO] DFAST Taxonomy check result was written to GCA_020852475.1_ASM2085247v1_genomic.fna/tc_result.tsv
[2023-06-28 17:30:10,643] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:30:10,643] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:30:10,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/checkm_data
[2023-06-28 17:30:10,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:30:10,675] [INFO] Task started: CheckM
[2023-06-28 17:30:10,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020852475.1_ASM2085247v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020852475.1_ASM2085247v1_genomic.fna/checkm_input GCA_020852475.1_ASM2085247v1_genomic.fna/checkm_result
[2023-06-28 17:30:36,969] [INFO] Task succeeded: CheckM
[2023-06-28 17:30:36,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:30:36,989] [INFO] ===== Completeness check finished =====
[2023-06-28 17:30:36,989] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:30:36,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020852475.1_ASM2085247v1_genomic.fna/markers.fasta)
[2023-06-28 17:30:36,990] [INFO] Task started: Blastn
[2023-06-28 17:30:36,990] [INFO] Running command: blastn -query GCA_020852475.1_ASM2085247v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0deaf28-5d32-4012-99f4-727d2a3a7019/dqc_reference/reference_markers_gtdb.fasta -out GCA_020852475.1_ASM2085247v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:30:37,914] [INFO] Task succeeded: Blastn
[2023-06-28 17:30:37,918] [INFO] Selected 26 target genomes.
[2023-06-28 17:30:37,919] [INFO] Target genome list was writen to GCA_020852475.1_ASM2085247v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:30:37,947] [INFO] Task started: fastANI
[2023-06-28 17:30:37,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b5a6dea-7da4-4a7f-9ec0-9aa9876c00af/GCA_020852475.1_ASM2085247v1_genomic.fna.gz --refList GCA_020852475.1_ASM2085247v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020852475.1_ASM2085247v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:30:49,888] [INFO] Task succeeded: fastANI
[2023-06-28 17:30:49,901] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:30:49,901] [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_015709615.1	s__Nitrosomonas sp015709615	78.358	106	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.12	98.12	0.95	0.95	2	-
GCA_902826055.1	s__Nitrosomonas sp902826055	77.5676	51	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111165.1	s__Nitrosomonas sp900111165	77.5449	132	881	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	77.4996	121	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.27	97.27	0.85	0.85	2	-
GCF_009833095.1	s__Nitrosomonas sp009833095	77.3517	73	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.87	99.87	0.93	0.93	2	-
GCF_004345375.1	s__Nitrosomonas sp004345375	77.3349	112	881	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	77.305	70	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	98.53	97.95	0.91	0.88	6	-
GCA_002083595.1	s__Nitrosomonas sp002083595	77.1235	104	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721865.1	s__Nitrosomonas sp016721865	77.0884	74	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003011925.2	s__Nitrosomonas sp003011925	77.0566	64	881	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	77.0087	119	881	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	76.9991	75	881	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	76.9916	90	881	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	76.8888	77	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003046585.1	s__Nitrosomonas aestuarii	76.5544	154	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	97.25	97.25	0.92	0.92	2	-
GCA_017984435.1	s__Nitrosomonas sp017984435	76.3672	86	881	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-28 17:30:49,904] [INFO] GTDB search result was written to GCA_020852475.1_ASM2085247v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:30:49,904] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:30:49,908] [INFO] DFAST_QC result json was written to GCA_020852475.1_ASM2085247v1_genomic.fna/dqc_result.json
[2023-06-28 17:30:49,908] [INFO] DFAST_QC completed!
[2023-06-28 17:30:49,908] [INFO] Total running time: 0h1m2s