[2024-01-24 13:25:29,515] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,519] [INFO] DQC Reference Directory: /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference
[2024-01-24 13:25:30,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,829] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,830] [INFO] Running command: gunzip -c /var/lib/cwl/stgca7dee84-9f42-45e1-841c-345d3a94cc5e/GCF_001552885.1_ASM155288v1_genomic.fna.gz | prodigal -d GCF_001552885.1_ASM155288v1_genomic.fna/cds.fna -a GCF_001552885.1_ASM155288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:34,287] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:34,287] [INFO] Task started: HMMsearch
[2024-01-24 13:25:34,287] [INFO] Running command: hmmsearch --tblout GCF_001552885.1_ASM155288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/reference_markers.hmm GCF_001552885.1_ASM155288v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:34,542] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:34,543] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgca7dee84-9f42-45e1-841c-345d3a94cc5e/GCF_001552885.1_ASM155288v1_genomic.fna.gz]
[2024-01-24 13:25:34,566] [INFO] Query marker FASTA was written to GCF_001552885.1_ASM155288v1_genomic.fna/markers.fasta
[2024-01-24 13:25:34,566] [INFO] Task started: Blastn
[2024-01-24 13:25:34,566] [INFO] Running command: blastn -query GCF_001552885.1_ASM155288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/reference_markers.fasta -out GCF_001552885.1_ASM155288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:35,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:35,187] [INFO] Selected 18 target genomes.
[2024-01-24 13:25:35,188] [INFO] Target genome list was writen to GCF_001552885.1_ASM155288v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:35,204] [INFO] Task started: fastANI
[2024-01-24 13:25:35,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgca7dee84-9f42-45e1-841c-345d3a94cc5e/GCF_001552885.1_ASM155288v1_genomic.fna.gz --refList GCF_001552885.1_ASM155288v1_genomic.fna/target_genomes.txt --output GCF_001552885.1_ASM155288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:43,882] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:43,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:43,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:43,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:25:43,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:25:43,884] [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
--------------------------------------------------------------------------------
[2024-01-24 13:25:43,885] [INFO] DFAST Taxonomy check result was written to GCF_001552885.1_ASM155288v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:43,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:43,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:43,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/checkm_data
[2024-01-24 13:25:43,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:43,912] [INFO] Task started: CheckM
[2024-01-24 13:25:43,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552885.1_ASM155288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552885.1_ASM155288v1_genomic.fna/checkm_input GCF_001552885.1_ASM155288v1_genomic.fna/checkm_result
[2024-01-24 13:26:01,970] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:01,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:01,988] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:01,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:01,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552885.1_ASM155288v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:01,990] [INFO] Task started: Blastn
[2024-01-24 13:26:01,990] [INFO] Running command: blastn -query GCF_001552885.1_ASM155288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60dcc1a1-9c24-45cf-9f8e-b9e8772d29fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552885.1_ASM155288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:02,958] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:02,963] [INFO] Selected 25 target genomes.
[2024-01-24 13:26:02,963] [INFO] Target genome list was writen to GCF_001552885.1_ASM155288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:03,015] [INFO] Task started: fastANI
[2024-01-24 13:26:03,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgca7dee84-9f42-45e1-841c-345d3a94cc5e/GCF_001552885.1_ASM155288v1_genomic.fna.gz --refList GCF_001552885.1_ASM155288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552885.1_ASM155288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:13,073] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:13,080] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:13,080] [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_001552885.1	s__KA00274 sp001552885	100.0	498	500	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Fastidiosipilaceae;g__KA00274	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902373515.1	s__KA00274 sp902373515	78.0167	75	500	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Fastidiosipilaceae;g__KA00274	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:13,082] [INFO] GTDB search result was written to GCF_001552885.1_ASM155288v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:13,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:13,087] [INFO] DFAST_QC result json was written to GCF_001552885.1_ASM155288v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:13,087] [INFO] DFAST_QC completed!
[2024-01-24 13:26:13,087] [INFO] Total running time: 0h0m44s