[2024-01-24 15:10:36,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:36,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:36,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference
[2024-01-24 15:10:40,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,099] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,099] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a56a2e5-db5a-48ee-9bd4-5aff0ed48146/GCF_013407145.1_ASM1340714v1_genomic.fna.gz | prodigal -d GCF_013407145.1_ASM1340714v1_genomic.fna/cds.fna -a GCF_013407145.1_ASM1340714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:43,403] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:43,404] [INFO] Task started: HMMsearch
[2024-01-24 15:10:43,404] [INFO] Running command: hmmsearch --tblout GCF_013407145.1_ASM1340714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/reference_markers.hmm GCF_013407145.1_ASM1340714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:43,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:43,675] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg4a56a2e5-db5a-48ee-9bd4-5aff0ed48146/GCF_013407145.1_ASM1340714v1_genomic.fna.gz]
[2024-01-24 15:10:43,694] [INFO] Query marker FASTA was written to GCF_013407145.1_ASM1340714v1_genomic.fna/markers.fasta
[2024-01-24 15:10:43,695] [INFO] Task started: Blastn
[2024-01-24 15:10:43,695] [INFO] Running command: blastn -query GCF_013407145.1_ASM1340714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/reference_markers.fasta -out GCF_013407145.1_ASM1340714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:46,468] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:46,470] [INFO] Selected 4 target genomes.
[2024-01-24 15:10:46,471] [INFO] Target genome list was writen to GCF_013407145.1_ASM1340714v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:46,474] [INFO] Task started: fastANI
[2024-01-24 15:10:46,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a56a2e5-db5a-48ee-9bd4-5aff0ed48146/GCF_013407145.1_ASM1340714v1_genomic.fna.gz --refList GCF_013407145.1_ASM1340714v1_genomic.fna/target_genomes.txt --output GCF_013407145.1_ASM1340714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:48,440] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:48,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:48,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:48,446] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:48,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:48,447] [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
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	100.0	521	521	95	conclusive
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	85.1359	424	521	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	81.7948	370	521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:48,450] [INFO] DFAST Taxonomy check result was written to GCF_013407145.1_ASM1340714v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:48,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:48,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:48,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/checkm_data
[2024-01-24 15:10:48,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:48,483] [INFO] Task started: CheckM
[2024-01-24 15:10:48,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407145.1_ASM1340714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407145.1_ASM1340714v1_genomic.fna/checkm_input GCF_013407145.1_ASM1340714v1_genomic.fna/checkm_result
[2024-01-24 15:11:09,372] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:09,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:09,392] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:09,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:09,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407145.1_ASM1340714v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:09,394] [INFO] Task started: Blastn
[2024-01-24 15:11:09,394] [INFO] Running command: blastn -query GCF_013407145.1_ASM1340714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1de5ce34-fad2-42e5-aab1-97bfbf831ad4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407145.1_ASM1340714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:09,875] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:09,880] [INFO] Selected 5 target genomes.
[2024-01-24 15:11:09,880] [INFO] Target genome list was writen to GCF_013407145.1_ASM1340714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:09,885] [INFO] Task started: fastANI
[2024-01-24 15:11:09,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a56a2e5-db5a-48ee-9bd4-5aff0ed48146/GCF_013407145.1_ASM1340714v1_genomic.fna.gz --refList GCF_013407145.1_ASM1340714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407145.1_ASM1340714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:12,093] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:12,101] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:12,101] [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_013407145.1	s__Nitrosopumilus cobalaminigenes	100.0	521	521	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013043295.1	s__Nitrosopumilus sp013043295	84.7254	277	521	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	100.00	100.00	0.98	0.98	2	-
GCA_013203245.1	s__Nitrosopumilus sp013203245	84.2935	304	521	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014078525.1	s__Nitrosopumilus sp014078525	81.926	353	521	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956175.1	s__Nitrosopumilus adriaticus	81.8149	369	521	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:12,103] [INFO] GTDB search result was written to GCF_013407145.1_ASM1340714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:12,103] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:12,106] [INFO] DFAST_QC result json was written to GCF_013407145.1_ASM1340714v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:12,106] [INFO] DFAST_QC completed!
[2024-01-24 15:11:12,106] [INFO] Total running time: 0h0m36s