[2023-06-13 05:12:50,454] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:12:50,458] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:12:50,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference
[2023-06-13 05:12:51,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:12:51,738] [INFO] Task started: Prodigal
[2023-06-13 05:12:51,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e69d3b2-5c63-49f7-917d-3aad94a28120/GCA_006954445.1_ASM695444v1_genomic.fna.gz | prodigal -d GCA_006954445.1_ASM695444v1_genomic.fna/cds.fna -a GCA_006954445.1_ASM695444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:12:55,990] [INFO] Task succeeded: Prodigal
[2023-06-13 05:12:55,991] [INFO] Task started: HMMsearch
[2023-06-13 05:12:55,991] [INFO] Running command: hmmsearch --tblout GCA_006954445.1_ASM695444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/reference_markers.hmm GCA_006954445.1_ASM695444v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:12:56,226] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:12:56,227] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7e69d3b2-5c63-49f7-917d-3aad94a28120/GCA_006954445.1_ASM695444v1_genomic.fna.gz]
[2023-06-13 05:12:56,251] [INFO] Query marker FASTA was written to GCA_006954445.1_ASM695444v1_genomic.fna/markers.fasta
[2023-06-13 05:12:56,251] [INFO] Task started: Blastn
[2023-06-13 05:12:56,252] [INFO] Running command: blastn -query GCA_006954445.1_ASM695444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/reference_markers.fasta -out GCA_006954445.1_ASM695444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:12:56,732] [INFO] Task succeeded: Blastn
[2023-06-13 05:12:56,736] [INFO] Selected 5 target genomes.
[2023-06-13 05:12:56,736] [INFO] Target genome list was writen to GCA_006954445.1_ASM695444v1_genomic.fna/target_genomes.txt
[2023-06-13 05:12:56,762] [INFO] Task started: fastANI
[2023-06-13 05:12:56,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e69d3b2-5c63-49f7-917d-3aad94a28120/GCA_006954445.1_ASM695444v1_genomic.fna.gz --refList GCA_006954445.1_ASM695444v1_genomic.fna/target_genomes.txt --output GCA_006954445.1_ASM695444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:12:58,972] [INFO] Task succeeded: fastANI
[2023-06-13 05:12:58,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:12:58,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:12:58,975] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:12:58,975] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:12:58,975] [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
--------------------------------------------------------------------------------
[2023-06-13 05:12:58,977] [INFO] DFAST Taxonomy check result was written to GCA_006954445.1_ASM695444v1_genomic.fna/tc_result.tsv
[2023-06-13 05:12:58,977] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:12:58,977] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:12:58,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/checkm_data
[2023-06-13 05:12:58,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:12:59,006] [INFO] Task started: CheckM
[2023-06-13 05:12:59,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_006954445.1_ASM695444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_006954445.1_ASM695444v1_genomic.fna/checkm_input GCA_006954445.1_ASM695444v1_genomic.fna/checkm_result
[2023-06-13 05:13:20,365] [INFO] Task succeeded: CheckM
[2023-06-13 05:13:20,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:13:20,383] [INFO] ===== Completeness check finished =====
[2023-06-13 05:13:20,383] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:13:20,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_006954445.1_ASM695444v1_genomic.fna/markers.fasta)
[2023-06-13 05:13:20,384] [INFO] Task started: Blastn
[2023-06-13 05:13:20,384] [INFO] Running command: blastn -query GCA_006954445.1_ASM695444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e4be0bb-ba89-4e9a-9e8e-0c4aa0a9b13a/dqc_reference/reference_markers_gtdb.fasta -out GCA_006954445.1_ASM695444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:13:20,869] [INFO] Task succeeded: Blastn
[2023-06-13 05:13:20,875] [INFO] Selected 6 target genomes.
[2023-06-13 05:13:20,875] [INFO] Target genome list was writen to GCA_006954445.1_ASM695444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:13:20,882] [INFO] Task started: fastANI
[2023-06-13 05:13:20,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e69d3b2-5c63-49f7-917d-3aad94a28120/GCA_006954445.1_ASM695444v1_genomic.fna.gz --refList GCA_006954445.1_ASM695444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_006954445.1_ASM695444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:13:22,998] [INFO] Task succeeded: fastANI
[2023-06-13 05:13:23,002] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:13:23,002] [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_000404225.1	s__Methanomassiliicoccus_A intestinalis	99.703	594	600	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__Methanomassiliicoccus_A	95.0	99.34	98.69	0.98	0.96	5	conclusive
GCA_905202485.1	s__Methanomassiliicoccus_A sp905202485	84.073	456	600	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomassiliicoccaceae;g__Methanomassiliicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:13:23,004] [INFO] GTDB search result was written to GCA_006954445.1_ASM695444v1_genomic.fna/result_gtdb.tsv
[2023-06-13 05:13:23,005] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:13:23,008] [INFO] DFAST_QC result json was written to GCA_006954445.1_ASM695444v1_genomic.fna/dqc_result.json
[2023-06-13 05:13:23,008] [INFO] DFAST_QC completed!
[2023-06-13 05:13:23,008] [INFO] Total running time: 0h0m33s