[2024-01-25 18:02:06,137] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:06,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:06,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference
[2024-01-25 18:02:07,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:07,348] [INFO] Task started: Prodigal
[2024-01-25 18:02:07,348] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0597169-3a28-4859-b114-235d82a6edc7/GCF_000196355.1_ASM19635v1_genomic.fna.gz | prodigal -d GCF_000196355.1_ASM19635v1_genomic.fna/cds.fna -a GCF_000196355.1_ASM19635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:17,001] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:17,001] [INFO] Task started: HMMsearch
[2024-01-25 18:02:17,001] [INFO] Running command: hmmsearch --tblout GCF_000196355.1_ASM19635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/reference_markers.hmm GCF_000196355.1_ASM19635v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:17,208] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:17,209] [INFO] Found 6/6 markers.
[2024-01-25 18:02:17,236] [INFO] Query marker FASTA was written to GCF_000196355.1_ASM19635v1_genomic.fna/markers.fasta
[2024-01-25 18:02:17,236] [INFO] Task started: Blastn
[2024-01-25 18:02:17,236] [INFO] Running command: blastn -query GCF_000196355.1_ASM19635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/reference_markers.fasta -out GCF_000196355.1_ASM19635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:17,814] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:17,818] [INFO] Selected 21 target genomes.
[2024-01-25 18:02:17,818] [INFO] Target genome list was writen to GCF_000196355.1_ASM19635v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:17,832] [INFO] Task started: fastANI
[2024-01-25 18:02:17,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0597169-3a28-4859-b114-235d82a6edc7/GCF_000196355.1_ASM19635v1_genomic.fna.gz --refList GCF_000196355.1_ASM19635v1_genomic.fna/target_genomes.txt --output GCF_000196355.1_ASM19635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:32,471] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:32,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:32,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:32,476] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:02:32,476] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:02:32,476] [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
Nitrosospira multiformis	strain=ATCC 25196	GCA_000196355.1	1231	1231	suspected-type	True	100.0	1074	1076	95	conclusive
Nitrosospira lacus	strain=APG3	GCA_000355765.4	1288494	1288494	type	True	77.7866	213	1076	95	below_threshold
Nitrosospira briensis	strain=C-128	GCA_000619905.2	35799	35799	reftype	True	77.6512	266	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:32,478] [INFO] DFAST Taxonomy check result was written to GCF_000196355.1_ASM19635v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:32,479] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:32,479] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:32,479] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/checkm_data
[2024-01-25 18:02:32,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:32,512] [INFO] Task started: CheckM
[2024-01-25 18:02:32,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196355.1_ASM19635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196355.1_ASM19635v1_genomic.fna/checkm_input GCF_000196355.1_ASM19635v1_genomic.fna/checkm_result
[2024-01-25 18:03:06,689] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:06,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:06,717] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:06,717] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:06,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196355.1_ASM19635v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:06,718] [INFO] Task started: Blastn
[2024-01-25 18:03:06,718] [INFO] Running command: blastn -query GCF_000196355.1_ASM19635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dbd09a8-e150-4828-9de1-8a6b5ba280d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196355.1_ASM19635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:07,624] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:07,626] [INFO] Selected 5 target genomes.
[2024-01-25 18:03:07,627] [INFO] Target genome list was writen to GCF_000196355.1_ASM19635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:07,633] [INFO] Task started: fastANI
[2024-01-25 18:03:07,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0597169-3a28-4859-b114-235d82a6edc7/GCF_000196355.1_ASM19635v1_genomic.fna.gz --refList GCF_000196355.1_ASM19635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196355.1_ASM19635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:11,976] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:11,980] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:11,980] [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_000196355.1	s__Nitrosospira multiformis	100.0	1074	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	99.45	98.91	0.96	0.92	3	conclusive
GCF_900111585.1	s__Nitrosospira multiformis_B	93.5805	919	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110185.1	s__Nitrosospira multiformis_A	93.124	904	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268875.1	s__Nitrosospira multiformis_E	91.0253	893	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	96.99	96.55	0.88	0.86	6	-
GCA_017306155.1	s__Nitrosospira multiformis_F	89.2415	847	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:11,982] [INFO] GTDB search result was written to GCF_000196355.1_ASM19635v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:11,982] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:11,984] [INFO] DFAST_QC result json was written to GCF_000196355.1_ASM19635v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:11,984] [INFO] DFAST_QC completed!
[2024-01-25 18:03:11,984] [INFO] Total running time: 0h1m6s