[2023-06-13 01:25:08,063] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:25:08,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:25:08,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgb52725ac-f29d-42eb-a679-16b534520882/dqc_reference
[2023-06-13 01:25:09,446] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:25:09,447] [INFO] Task started: Prodigal
[2023-06-13 01:25:09,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e89034e-4ec5-42a9-a7bd-452ab9e04866/GCA_022014875.1_ASM2201487v1_genomic.fna.gz | prodigal -d GCA_022014875.1_ASM2201487v1_genomic.fna/cds.fna -a GCA_022014875.1_ASM2201487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:25:15,001] [INFO] Task succeeded: Prodigal
[2023-06-13 01:25:15,001] [INFO] Task started: HMMsearch
[2023-06-13 01:25:15,001] [INFO] Running command: hmmsearch --tblout GCA_022014875.1_ASM2201487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb52725ac-f29d-42eb-a679-16b534520882/dqc_reference/reference_markers.hmm GCA_022014875.1_ASM2201487v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:25:15,227] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:25:15,228] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2e89034e-4ec5-42a9-a7bd-452ab9e04866/GCA_022014875.1_ASM2201487v1_genomic.fna.gz]
[2023-06-13 01:25:15,243] [INFO] Query marker FASTA was written to GCA_022014875.1_ASM2201487v1_genomic.fna/markers.fasta
[2023-06-13 01:25:15,244] [INFO] Task started: Blastn
[2023-06-13 01:25:15,244] [INFO] Running command: blastn -query GCA_022014875.1_ASM2201487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52725ac-f29d-42eb-a679-16b534520882/dqc_reference/reference_markers.fasta -out GCA_022014875.1_ASM2201487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:25:15,773] [INFO] Task succeeded: Blastn
[2023-06-13 01:25:15,776] [INFO] Selected 0 target genomes.
[2023-06-13 01:25:15,776] [INFO] Target genome list was writen to GCA_022014875.1_ASM2201487v1_genomic.fna/target_genomes.txt
[2023-06-13 01:25:15,777] [ERROR] File is empty. [GCA_022014875.1_ASM2201487v1_genomic.fna/target_genomes.txt]
[2023-06-13 01:25:15,777] [ERROR] Task failed. No target genome found.
[2023-06-13 01:25:15,777] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:25:15,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb52725ac-f29d-42eb-a679-16b534520882/dqc_reference/checkm_data
[2023-06-13 01:25:15,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:25:15,801] [INFO] Task started: CheckM
[2023-06-13 01:25:15,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022014875.1_ASM2201487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022014875.1_ASM2201487v1_genomic.fna/checkm_input GCA_022014875.1_ASM2201487v1_genomic.fna/checkm_result
[2023-06-13 01:25:38,539] [INFO] Task succeeded: CheckM
[2023-06-13 01:25:38,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:25:38,560] [INFO] ===== Completeness check finished =====
[2023-06-13 01:25:38,561] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:25:38,561] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022014875.1_ASM2201487v1_genomic.fna/markers.fasta)
[2023-06-13 01:25:38,561] [INFO] Task started: Blastn
[2023-06-13 01:25:38,562] [INFO] Running command: blastn -query GCA_022014875.1_ASM2201487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb52725ac-f29d-42eb-a679-16b534520882/dqc_reference/reference_markers_gtdb.fasta -out GCA_022014875.1_ASM2201487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:25:39,111] [INFO] Task succeeded: Blastn
[2023-06-13 01:25:39,114] [INFO] Selected 2 target genomes.
[2023-06-13 01:25:39,115] [INFO] Target genome list was writen to GCA_022014875.1_ASM2201487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:25:39,117] [INFO] Task started: fastANI
[2023-06-13 01:25:39,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e89034e-4ec5-42a9-a7bd-452ab9e04866/GCA_022014875.1_ASM2201487v1_genomic.fna.gz --refList GCA_022014875.1_ASM2201487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022014875.1_ASM2201487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:25:39,999] [INFO] Task succeeded: fastANI
[2023-06-13 01:25:40,006] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:25:40,007] [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_001316265.1	s__Vulcanisaeta sp001316265	77.1525	110	373	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001315985.1	s__Vulcanisaeta distributa_E	76.8651	114	373	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Thermoproteales;f__Thermocladiaceae;g__Vulcanisaeta	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:25:40,009] [INFO] GTDB search result was written to GCA_022014875.1_ASM2201487v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:25:40,011] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:25:40,013] [INFO] DFAST_QC result json was written to GCA_022014875.1_ASM2201487v1_genomic.fna/dqc_result.json
[2023-06-13 01:25:40,014] [INFO] DFAST_QC completed!
[2023-06-13 01:25:40,014] [INFO] Total running time: 0h0m32s