[2024-01-25 18:47:05,875] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:05,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:05,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference
[2024-01-25 18:47:07,006] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:07,006] [INFO] Task started: Prodigal
[2024-01-25 18:47:07,007] [INFO] Running command: gunzip -c /var/lib/cwl/stg74b3fa12-f7b3-4b9d-800c-94883054e6e4/GCF_000220175.1_ASM22017v1_genomic.fna.gz | prodigal -d GCF_000220175.1_ASM22017v1_genomic.fna/cds.fna -a GCF_000220175.1_ASM22017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:09,872] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:09,872] [INFO] Task started: HMMsearch
[2024-01-25 18:47:09,872] [INFO] Running command: hmmsearch --tblout GCF_000220175.1_ASM22017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/reference_markers.hmm GCF_000220175.1_ASM22017v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:09,998] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:09,999] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg74b3fa12-f7b3-4b9d-800c-94883054e6e4/GCF_000220175.1_ASM22017v1_genomic.fna.gz]
[2024-01-25 18:47:10,018] [INFO] Query marker FASTA was written to GCF_000220175.1_ASM22017v1_genomic.fna/markers.fasta
[2024-01-25 18:47:10,018] [INFO] Task started: Blastn
[2024-01-25 18:47:10,018] [INFO] Running command: blastn -query GCF_000220175.1_ASM22017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/reference_markers.fasta -out GCF_000220175.1_ASM22017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:10,439] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:10,442] [INFO] Selected 2 target genomes.
[2024-01-25 18:47:10,442] [INFO] Target genome list was writen to GCF_000220175.1_ASM22017v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:10,445] [INFO] Task started: fastANI
[2024-01-25 18:47:10,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b3fa12-f7b3-4b9d-800c-94883054e6e4/GCF_000220175.1_ASM22017v1_genomic.fna.gz --refList GCF_000220175.1_ASM22017v1_genomic.fna/target_genomes.txt --output GCF_000220175.1_ASM22017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:11,120] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:11,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:11,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:11,124] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:11,124] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:11,124] [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	79.2995	288	535	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	79.1245	268	535	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:11,126] [INFO] DFAST Taxonomy check result was written to GCF_000220175.1_ASM22017v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:11,126] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:11,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:11,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/checkm_data
[2024-01-25 18:47:11,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:11,145] [INFO] Task started: CheckM
[2024-01-25 18:47:11,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000220175.1_ASM22017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000220175.1_ASM22017v1_genomic.fna/checkm_input GCF_000220175.1_ASM22017v1_genomic.fna/checkm_result
[2024-01-25 18:47:26,386] [INFO] Task succeeded: CheckM
[2024-01-25 18:47:26,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:47:26,407] [INFO] ===== Completeness check finished =====
[2024-01-25 18:47:26,407] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:47:26,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000220175.1_ASM22017v1_genomic.fna/markers.fasta)
[2024-01-25 18:47:26,407] [INFO] Task started: Blastn
[2024-01-25 18:47:26,407] [INFO] Running command: blastn -query GCF_000220175.1_ASM22017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16e2f478-5f0e-45bd-93ad-ca46470b4971/dqc_reference/reference_markers_gtdb.fasta -out GCF_000220175.1_ASM22017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:26,801] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:26,803] [INFO] Selected 5 target genomes.
[2024-01-25 18:47:26,803] [INFO] Target genome list was writen to GCF_000220175.1_ASM22017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:47:26,809] [INFO] Task started: fastANI
[2024-01-25 18:47:26,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg74b3fa12-f7b3-4b9d-800c-94883054e6e4/GCF_000220175.1_ASM22017v1_genomic.fna.gz --refList GCF_000220175.1_ASM22017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000220175.1_ASM22017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:47:28,598] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:28,603] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:47:28,603] [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_000220175.1	s__Nitrosarchaeum koreense	100.0	535	535	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	96.71	96.71	0.93	0.93	2	conclusive
GCA_018334095.1	s__Nitrosarchaeum sp018334095	92.2769	407	535	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697485.1	s__Nitrosarchaeum sp009697485	84.5928	176	535	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003569705.1	s__Nitrosarchaeum sp003569705	84.0406	386	535	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	99.59	99.59	0.99	0.99	2	-
GCA_013140415.1	s__Nitrosarchaeum sp013140415	83.825	258	535	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:47:28,605] [INFO] GTDB search result was written to GCF_000220175.1_ASM22017v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:47:28,605] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:47:28,608] [INFO] DFAST_QC result json was written to GCF_000220175.1_ASM22017v1_genomic.fna/dqc_result.json
[2024-01-25 18:47:28,608] [INFO] DFAST_QC completed!
[2024-01-25 18:47:28,608] [INFO] Total running time: 0h0m23s