[2023-06-18 20:56:02,822] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:02,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:02,824] [INFO] DQC Reference Directory: /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference
[2023-06-18 20:56:04,740] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:04,741] [INFO] Task started: Prodigal
[2023-06-18 20:56:04,742] [INFO] Running command: gunzip -c /var/lib/cwl/stg90f1a7d8-167e-4b70-94c1-71d8d63aaa60/GCA_018819865.1_ASM1881986v1_genomic.fna.gz | prodigal -d GCA_018819865.1_ASM1881986v1_genomic.fna/cds.fna -a GCA_018819865.1_ASM1881986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:07,204] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:07,205] [INFO] Task started: HMMsearch
[2023-06-18 20:56:07,205] [INFO] Running command: hmmsearch --tblout GCA_018819865.1_ASM1881986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/reference_markers.hmm GCA_018819865.1_ASM1881986v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:07,397] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:07,399] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90f1a7d8-167e-4b70-94c1-71d8d63aaa60/GCA_018819865.1_ASM1881986v1_genomic.fna.gz]
[2023-06-18 20:56:07,420] [INFO] Query marker FASTA was written to GCA_018819865.1_ASM1881986v1_genomic.fna/markers.fasta
[2023-06-18 20:56:07,421] [INFO] Task started: Blastn
[2023-06-18 20:56:07,421] [INFO] Running command: blastn -query GCA_018819865.1_ASM1881986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/reference_markers.fasta -out GCA_018819865.1_ASM1881986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:08,726] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:08,733] [INFO] Selected 10 target genomes.
[2023-06-18 20:56:08,734] [INFO] Target genome list was writen to GCA_018819865.1_ASM1881986v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:08,738] [INFO] Task started: fastANI
[2023-06-18 20:56:08,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f1a7d8-167e-4b70-94c1-71d8d63aaa60/GCA_018819865.1_ASM1881986v1_genomic.fna.gz --refList GCA_018819865.1_ASM1881986v1_genomic.fna/target_genomes.txt --output GCA_018819865.1_ASM1881986v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:13,986] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:13,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:13,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:13,989] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:13,989] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:56:13,990] [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
--------------------------------------------------------------------------------
[2023-06-18 20:56:13,992] [INFO] DFAST Taxonomy check result was written to GCA_018819865.1_ASM1881986v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:13,992] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:13,993] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:13,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/checkm_data
[2023-06-18 20:56:13,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:14,010] [INFO] Task started: CheckM
[2023-06-18 20:56:14,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018819865.1_ASM1881986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018819865.1_ASM1881986v1_genomic.fna/checkm_input GCA_018819865.1_ASM1881986v1_genomic.fna/checkm_result
[2023-06-18 20:56:29,093] [INFO] Task succeeded: CheckM
[2023-06-18 20:56:29,095] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:56:29,115] [INFO] ===== Completeness check finished =====
[2023-06-18 20:56:29,116] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:56:29,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018819865.1_ASM1881986v1_genomic.fna/markers.fasta)
[2023-06-18 20:56:29,117] [INFO] Task started: Blastn
[2023-06-18 20:56:29,117] [INFO] Running command: blastn -query GCA_018819865.1_ASM1881986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92ba41a-40dd-4eaa-a073-1c7d6006d658/dqc_reference/reference_markers_gtdb.fasta -out GCA_018819865.1_ASM1881986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:29,802] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:29,806] [INFO] Selected 8 target genomes.
[2023-06-18 20:56:29,807] [INFO] Target genome list was writen to GCA_018819865.1_ASM1881986v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:56:29,860] [INFO] Task started: fastANI
[2023-06-18 20:56:29,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg90f1a7d8-167e-4b70-94c1-71d8d63aaa60/GCA_018819865.1_ASM1881986v1_genomic.fna.gz --refList GCA_018819865.1_ASM1881986v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018819865.1_ASM1881986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:56:32,231] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:32,238] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:56:32,238] [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_018819325.1	s__JAHITH01 sp018819325	99.3687	126	140	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__JAHITH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018817845.1	s__JAHITH01 sp018817845	94.2544	87	140	d__Bacteria;p__Patescibacteria;c__Microgenomatia;o__UBA1400;f__MFAQ01;g__JAHITH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:56:32,240] [INFO] GTDB search result was written to GCA_018819865.1_ASM1881986v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:56:32,240] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:56:32,242] [INFO] DFAST_QC result json was written to GCA_018819865.1_ASM1881986v1_genomic.fna/dqc_result.json
[2023-06-18 20:56:32,242] [INFO] DFAST_QC completed!
[2023-06-18 20:56:32,242] [INFO] Total running time: 0h0m29s