[2024-01-24 12:13:41,648] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:41,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:41,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference
[2024-01-24 12:13:42,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:42,918] [INFO] Task started: Prodigal
[2024-01-24 12:13:42,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ddb53f1-5937-4e36-894a-7a03a9fb5f00/GCF_000341545.2_ASM34154v2_genomic.fna.gz | prodigal -d GCF_000341545.2_ASM34154v2_genomic.fna/cds.fna -a GCF_000341545.2_ASM34154v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:52,887] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:52,887] [INFO] Task started: HMMsearch
[2024-01-24 12:13:52,887] [INFO] Running command: hmmsearch --tblout GCF_000341545.2_ASM34154v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/reference_markers.hmm GCF_000341545.2_ASM34154v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:53,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:53,215] [INFO] Found 6/6 markers.
[2024-01-24 12:13:53,249] [INFO] Query marker FASTA was written to GCF_000341545.2_ASM34154v2_genomic.fna/markers.fasta
[2024-01-24 12:13:53,249] [INFO] Task started: Blastn
[2024-01-24 12:13:53,249] [INFO] Running command: blastn -query GCF_000341545.2_ASM34154v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/reference_markers.fasta -out GCF_000341545.2_ASM34154v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:54,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:54,030] [INFO] Selected 28 target genomes.
[2024-01-24 12:13:54,030] [INFO] Target genome list was writen to GCF_000341545.2_ASM34154v2_genomic.fna/target_genomes.txt
[2024-01-24 12:13:54,041] [INFO] Task started: fastANI
[2024-01-24 12:13:54,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ddb53f1-5937-4e36-894a-7a03a9fb5f00/GCF_000341545.2_ASM34154v2_genomic.fna.gz --refList GCF_000341545.2_ASM34154v2_genomic.fna/target_genomes.txt --output GCF_000341545.2_ASM34154v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:13,431] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:13,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:13,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:13,439] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:13,439] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:13,439] [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
Nitrospina gracilis	strain=3/211	GCA_000341545.2	35801	35801	type	True	100.0	1024	1024	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,444] [INFO] DFAST Taxonomy check result was written to GCF_000341545.2_ASM34154v2_genomic.fna/tc_result.tsv
[2024-01-24 12:14:13,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:13,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:13,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/checkm_data
[2024-01-24 12:14:13,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:13,478] [INFO] Task started: CheckM
[2024-01-24 12:14:13,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000341545.2_ASM34154v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000341545.2_ASM34154v2_genomic.fna/checkm_input GCF_000341545.2_ASM34154v2_genomic.fna/checkm_result
[2024-01-24 12:14:47,475] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:47,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:47,497] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:47,498] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:47,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000341545.2_ASM34154v2_genomic.fna/markers.fasta)
[2024-01-24 12:14:47,499] [INFO] Task started: Blastn
[2024-01-24 12:14:47,499] [INFO] Running command: blastn -query GCF_000341545.2_ASM34154v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a57fbe-be7a-40d7-a6fa-d08d184ea8a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000341545.2_ASM34154v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:48,860] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:48,867] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:48,868] [INFO] Target genome list was writen to GCF_000341545.2_ASM34154v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:48,931] [INFO] Task started: fastANI
[2024-01-24 12:14:48,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ddb53f1-5937-4e36-894a-7a03a9fb5f00/GCF_000341545.2_ASM34154v2_genomic.fna.gz --refList GCF_000341545.2_ASM34154v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000341545.2_ASM34154v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:04,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:04,714] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:04,714] [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_000341545.2	s__Nitrospina gracilis	100.0	1024	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitrospina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004357365.1	s__SZUA-226 sp004357365	77.1356	181	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__SZUA-226	95.0	97.52	97.52	0.74	0.74	2	-
GCA_003235465.1	s__SZUA-259 sp003235465	77.1309	122	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__SZUA-259	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003246675.1	s__SZUA-259 sp003246675	76.7821	139	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__SZUA-259	95.0	99.25	99.25	0.86	0.86	2	-
GCA_004357435.1	s__SMVS01 sp004357435	76.6397	88	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__SMVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015698305.1	s__Nitrohelix vancouverensis	76.5277	83	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitrohelix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003229345.1	s__SZUA-226 sp003229345	76.4484	68	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__SZUA-226	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015698285.1	s__Nitronauta litoralis	76.3514	59	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__Nitronauta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796165.1	s__21-14-0-20-56-8 sp002796165	76.22	95	1024	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__21-14-0-20-56-8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,716] [INFO] GTDB search result was written to GCF_000341545.2_ASM34154v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:04,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:04,720] [INFO] DFAST_QC result json was written to GCF_000341545.2_ASM34154v2_genomic.fna/dqc_result.json
[2024-01-24 12:15:04,720] [INFO] DFAST_QC completed!
[2024-01-24 12:15:04,720] [INFO] Total running time: 0h1m23s