[2023-06-29 10:06:32,390] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:06:32,392] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:06:32,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference
[2023-06-29 10:06:33,726] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:06:33,727] [INFO] Task started: Prodigal
[2023-06-29 10:06:33,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f7588c8-848d-41d3-a2b9-0a66b6a433b4/GCA_020048815.1_ASM2004881v1_genomic.fna.gz | prodigal -d GCA_020048815.1_ASM2004881v1_genomic.fna/cds.fna -a GCA_020048815.1_ASM2004881v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:06:43,785] [INFO] Task succeeded: Prodigal
[2023-06-29 10:06:43,786] [INFO] Task started: HMMsearch
[2023-06-29 10:06:43,786] [INFO] Running command: hmmsearch --tblout GCA_020048815.1_ASM2004881v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/reference_markers.hmm GCA_020048815.1_ASM2004881v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:06:44,017] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:06:44,024] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3f7588c8-848d-41d3-a2b9-0a66b6a433b4/GCA_020048815.1_ASM2004881v1_genomic.fna.gz]
[2023-06-29 10:06:44,054] [INFO] Query marker FASTA was written to GCA_020048815.1_ASM2004881v1_genomic.fna/markers.fasta
[2023-06-29 10:06:44,054] [INFO] Task started: Blastn
[2023-06-29 10:06:44,055] [INFO] Running command: blastn -query GCA_020048815.1_ASM2004881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/reference_markers.fasta -out GCA_020048815.1_ASM2004881v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:06:44,589] [INFO] Task succeeded: Blastn
[2023-06-29 10:06:44,593] [INFO] Selected 15 target genomes.
[2023-06-29 10:06:44,593] [INFO] Target genome list was writen to GCA_020048815.1_ASM2004881v1_genomic.fna/target_genomes.txt
[2023-06-29 10:06:44,601] [INFO] Task started: fastANI
[2023-06-29 10:06:44,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7588c8-848d-41d3-a2b9-0a66b6a433b4/GCA_020048815.1_ASM2004881v1_genomic.fna.gz --refList GCA_020048815.1_ASM2004881v1_genomic.fna/target_genomes.txt --output GCA_020048815.1_ASM2004881v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:06:51,905] [INFO] Task succeeded: fastANI
[2023-06-29 10:06:51,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:06:51,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:06:51,908] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:06:51,908] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 10:06:51,908] [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
--------------------------------------------------------------------------------
[2023-06-29 10:06:51,910] [INFO] DFAST Taxonomy check result was written to GCA_020048815.1_ASM2004881v1_genomic.fna/tc_result.tsv
[2023-06-29 10:06:51,911] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:06:51,911] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:06:51,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/checkm_data
[2023-06-29 10:06:51,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:06:51,948] [INFO] Task started: CheckM
[2023-06-29 10:06:51,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020048815.1_ASM2004881v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020048815.1_ASM2004881v1_genomic.fna/checkm_input GCA_020048815.1_ASM2004881v1_genomic.fna/checkm_result
[2023-06-29 10:07:25,892] [INFO] Task succeeded: CheckM
[2023-06-29 10:07:25,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.79%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:07:25,915] [INFO] ===== Completeness check finished =====
[2023-06-29 10:07:25,915] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:07:25,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020048815.1_ASM2004881v1_genomic.fna/markers.fasta)
[2023-06-29 10:07:25,916] [INFO] Task started: Blastn
[2023-06-29 10:07:25,916] [INFO] Running command: blastn -query GCA_020048815.1_ASM2004881v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b2fc05b-fd46-48f7-b9d7-072dbe59c0c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_020048815.1_ASM2004881v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:07:26,547] [INFO] Task succeeded: Blastn
[2023-06-29 10:07:26,552] [INFO] Selected 15 target genomes.
[2023-06-29 10:07:26,552] [INFO] Target genome list was writen to GCA_020048815.1_ASM2004881v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:07:26,568] [INFO] Task started: fastANI
[2023-06-29 10:07:26,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7588c8-848d-41d3-a2b9-0a66b6a433b4/GCA_020048815.1_ASM2004881v1_genomic.fna.gz --refList GCA_020048815.1_ASM2004881v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020048815.1_ASM2004881v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:07:34,556] [INFO] Task succeeded: fastANI
[2023-06-29 10:07:34,559] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:07:34,560] [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
--------------------------------------------------------------------------------
[2023-06-29 10:07:34,562] [INFO] GTDB search result was written to GCA_020048815.1_ASM2004881v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:07:34,563] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:07:34,566] [INFO] DFAST_QC result json was written to GCA_020048815.1_ASM2004881v1_genomic.fna/dqc_result.json
[2023-06-29 10:07:34,566] [INFO] DFAST_QC completed!
[2023-06-29 10:07:34,566] [INFO] Total running time: 0h1m2s