[2023-06-17 09:46:17,684] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:46:17,687] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:46:17,688] [INFO] DQC Reference Directory: /var/lib/cwl/stgc507ca50-f339-4f44-97af-6bb20d0a12b7/dqc_reference
[2023-06-17 09:46:18,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:46:18,996] [INFO] Task started: Prodigal
[2023-06-17 09:46:18,996] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcf390a5-65bf-4d6c-a934-6fff679181fc/GCA_009665175.1_ASM966517v1_genomic.fna.gz | prodigal -d GCA_009665175.1_ASM966517v1_genomic.fna/cds.fna -a GCA_009665175.1_ASM966517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:46:24,215] [INFO] Task succeeded: Prodigal
[2023-06-17 09:46:24,216] [INFO] Task started: HMMsearch
[2023-06-17 09:46:24,216] [INFO] Running command: hmmsearch --tblout GCA_009665175.1_ASM966517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc507ca50-f339-4f44-97af-6bb20d0a12b7/dqc_reference/reference_markers.hmm GCA_009665175.1_ASM966517v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:46:24,455] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:46:24,456] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdcf390a5-65bf-4d6c-a934-6fff679181fc/GCA_009665175.1_ASM966517v1_genomic.fna.gz]
[2023-06-17 09:46:24,496] [INFO] Query marker FASTA was written to GCA_009665175.1_ASM966517v1_genomic.fna/markers.fasta
[2023-06-17 09:46:24,496] [INFO] Task started: Blastn
[2023-06-17 09:46:24,496] [INFO] Running command: blastn -query GCA_009665175.1_ASM966517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc507ca50-f339-4f44-97af-6bb20d0a12b7/dqc_reference/reference_markers.fasta -out GCA_009665175.1_ASM966517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:46:24,987] [INFO] Task succeeded: Blastn
[2023-06-17 09:46:24,991] [INFO] Selected 0 target genomes.
[2023-06-17 09:46:24,991] [INFO] Target genome list was writen to GCA_009665175.1_ASM966517v1_genomic.fna/target_genomes.txt
[2023-06-17 09:46:24,992] [ERROR] File is empty. [GCA_009665175.1_ASM966517v1_genomic.fna/target_genomes.txt]
[2023-06-17 09:46:24,992] [ERROR] Task failed. No target genome found.
[2023-06-17 09:46:24,992] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:46:24,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc507ca50-f339-4f44-97af-6bb20d0a12b7/dqc_reference/checkm_data
[2023-06-17 09:46:24,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:46:25,014] [INFO] Task started: CheckM
[2023-06-17 09:46:25,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009665175.1_ASM966517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009665175.1_ASM966517v1_genomic.fna/checkm_input GCA_009665175.1_ASM966517v1_genomic.fna/checkm_result
[2023-06-17 09:46:48,932] [INFO] Task succeeded: CheckM
[2023-06-17 09:46:48,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.36%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 09:46:48,959] [INFO] ===== Completeness check finished =====
[2023-06-17 09:46:48,960] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:46:48,960] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009665175.1_ASM966517v1_genomic.fna/markers.fasta)
[2023-06-17 09:46:48,960] [INFO] Task started: Blastn
[2023-06-17 09:46:48,960] [INFO] Running command: blastn -query GCA_009665175.1_ASM966517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc507ca50-f339-4f44-97af-6bb20d0a12b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_009665175.1_ASM966517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:46:49,433] [INFO] Task succeeded: Blastn
[2023-06-17 09:46:49,437] [INFO] Selected 3 target genomes.
[2023-06-17 09:46:49,437] [INFO] Target genome list was writen to GCA_009665175.1_ASM966517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:46:49,439] [INFO] Task started: fastANI
[2023-06-17 09:46:49,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf390a5-65bf-4d6c-a934-6fff679181fc/GCA_009665175.1_ASM966517v1_genomic.fna.gz --refList GCA_009665175.1_ASM966517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009665175.1_ASM966517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:46:51,045] [INFO] Task succeeded: fastANI
[2023-06-17 09:46:51,052] [INFO] Found 3 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-17 09:46:51,052] [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_009665115.1	s__UBA10452 sp009665115	97.7875	168	189	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__UBA10452	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002501855.1	s__UBA10452 sp002501855	95.9669	171	189	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__UBA10452	95.0	99.20	99.10	0.81	0.78	6	inconclusive
GCA_003176995.1	s__UBA10452 sp003176995	94.6665	176	189	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrososphaeraceae;g__UBA10452	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:46:51,055] [INFO] GTDB search result was written to GCA_009665175.1_ASM966517v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:46:51,056] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:46:51,058] [INFO] DFAST_QC result json was written to GCA_009665175.1_ASM966517v1_genomic.fna/dqc_result.json
[2023-06-17 09:46:51,058] [INFO] DFAST_QC completed!
[2023-06-17 09:46:51,059] [INFO] Total running time: 0h0m33s