[2023-06-17 07:31:24,864] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:31:24,867] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:31:24,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg2593a70f-e296-4a86-8225-4c492341a86f/dqc_reference
[2023-06-17 07:31:26,876] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:31:26,877] [INFO] Task started: Prodigal
[2023-06-17 07:31:26,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ce52c2c-c77a-454a-a646-17cc0e0f8759/GCA_003556925.1_ASM355692v1_genomic.fna.gz | prodigal -d GCA_003556925.1_ASM355692v1_genomic.fna/cds.fna -a GCA_003556925.1_ASM355692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:31:27,908] [INFO] Task succeeded: Prodigal
[2023-06-17 07:31:27,908] [INFO] Task started: HMMsearch
[2023-06-17 07:31:27,909] [INFO] Running command: hmmsearch --tblout GCA_003556925.1_ASM355692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2593a70f-e296-4a86-8225-4c492341a86f/dqc_reference/reference_markers.hmm GCA_003556925.1_ASM355692v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:31:28,153] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:31:28,154] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7ce52c2c-c77a-454a-a646-17cc0e0f8759/GCA_003556925.1_ASM355692v1_genomic.fna.gz]
[2023-06-17 07:31:28,187] [INFO] Query marker FASTA was written to GCA_003556925.1_ASM355692v1_genomic.fna/markers.fasta
[2023-06-17 07:31:28,188] [INFO] Task started: Blastn
[2023-06-17 07:31:28,188] [INFO] Running command: blastn -query GCA_003556925.1_ASM355692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2593a70f-e296-4a86-8225-4c492341a86f/dqc_reference/reference_markers.fasta -out GCA_003556925.1_ASM355692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:30,542] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:30,546] [INFO] Selected 0 target genomes.
[2023-06-17 07:31:30,546] [INFO] Target genome list was writen to GCA_003556925.1_ASM355692v1_genomic.fna/target_genomes.txt
[2023-06-17 07:31:30,546] [ERROR] File is empty. [GCA_003556925.1_ASM355692v1_genomic.fna/target_genomes.txt]
[2023-06-17 07:31:30,546] [ERROR] Task failed. No target genome found.
[2023-06-17 07:31:30,546] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:31:30,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2593a70f-e296-4a86-8225-4c492341a86f/dqc_reference/checkm_data
[2023-06-17 07:31:30,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:31:30,563] [INFO] Task started: CheckM
[2023-06-17 07:31:30,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003556925.1_ASM355692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003556925.1_ASM355692v1_genomic.fna/checkm_input GCA_003556925.1_ASM355692v1_genomic.fna/checkm_result
[2023-06-17 07:31:42,904] [INFO] Task succeeded: CheckM
[2023-06-17 07:31:42,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.15%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 07:31:42,931] [INFO] ===== Completeness check finished =====
[2023-06-17 07:31:42,931] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:31:42,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003556925.1_ASM355692v1_genomic.fna/markers.fasta)
[2023-06-17 07:31:42,932] [INFO] Task started: Blastn
[2023-06-17 07:31:42,932] [INFO] Running command: blastn -query GCA_003556925.1_ASM355692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2593a70f-e296-4a86-8225-4c492341a86f/dqc_reference/reference_markers_gtdb.fasta -out GCA_003556925.1_ASM355692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:43,353] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:43,357] [INFO] Selected 12 target genomes.
[2023-06-17 07:31:43,358] [INFO] Target genome list was writen to GCA_003556925.1_ASM355692v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:31:43,367] [INFO] Task started: fastANI
[2023-06-17 07:31:43,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ce52c2c-c77a-454a-a646-17cc0e0f8759/GCA_003556925.1_ASM355692v1_genomic.fna.gz --refList GCA_003556925.1_ASM355692v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003556925.1_ASM355692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:31:47,383] [INFO] Task succeeded: fastANI
[2023-06-17 07:31:47,387] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:31:47,388] [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_003556925.1	s__PWMZ01 sp003556925	100.0	89	91	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__Paceibacterales;f__PWMZ01;g__PWMZ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-06-17 07:31:47,391] [INFO] GTDB search result was written to GCA_003556925.1_ASM355692v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:31:47,392] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:31:47,395] [INFO] DFAST_QC result json was written to GCA_003556925.1_ASM355692v1_genomic.fna/dqc_result.json
[2023-06-17 07:31:47,395] [INFO] DFAST_QC completed!
[2023-06-17 07:31:47,396] [INFO] Total running time: 0h0m23s