[2023-06-30 18:39:30,893] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:39:30,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:39:30,895] [INFO] DQC Reference Directory: /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference
[2023-06-30 18:39:34,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:39:34,256] [INFO] Task started: Prodigal
[2023-06-30 18:39:34,256] [INFO] Running command: gunzip -c /var/lib/cwl/stgee2223c9-8994-403c-9c29-92bd811fcee5/GCA_900762145.1_SRS1170747_9_genomic.fna.gz | prodigal -d GCA_900762145.1_SRS1170747_9_genomic.fna/cds.fna -a GCA_900762145.1_SRS1170747_9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:39:38,591] [INFO] Task succeeded: Prodigal
[2023-06-30 18:39:38,591] [INFO] Task started: HMMsearch
[2023-06-30 18:39:38,591] [INFO] Running command: hmmsearch --tblout GCA_900762145.1_SRS1170747_9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/reference_markers.hmm GCA_900762145.1_SRS1170747_9_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:39:38,887] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:39:38,888] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgee2223c9-8994-403c-9c29-92bd811fcee5/GCA_900762145.1_SRS1170747_9_genomic.fna.gz]
[2023-06-30 18:39:38,924] [INFO] Query marker FASTA was written to GCA_900762145.1_SRS1170747_9_genomic.fna/markers.fasta
[2023-06-30 18:39:38,925] [INFO] Task started: Blastn
[2023-06-30 18:39:38,925] [INFO] Running command: blastn -query GCA_900762145.1_SRS1170747_9_genomic.fna/markers.fasta -db /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/reference_markers.fasta -out GCA_900762145.1_SRS1170747_9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:39:40,827] [INFO] Task succeeded: Blastn
[2023-06-30 18:39:40,831] [INFO] Selected 20 target genomes.
[2023-06-30 18:39:40,831] [INFO] Target genome list was writen to GCA_900762145.1_SRS1170747_9_genomic.fna/target_genomes.txt
[2023-06-30 18:39:40,832] [INFO] Task started: fastANI
[2023-06-30 18:39:40,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgee2223c9-8994-403c-9c29-92bd811fcee5/GCA_900762145.1_SRS1170747_9_genomic.fna.gz --refList GCA_900762145.1_SRS1170747_9_genomic.fna/target_genomes.txt --output GCA_900762145.1_SRS1170747_9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:39:49,784] [INFO] Task succeeded: fastANI
[2023-06-30 18:39:49,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:39:49,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:39:49,786] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:39:49,786] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 18:39:49,786] [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
--------------------------------------------------------------------------------
[2023-06-30 18:39:49,788] [INFO] DFAST Taxonomy check result was written to GCA_900762145.1_SRS1170747_9_genomic.fna/tc_result.tsv
[2023-06-30 18:39:49,788] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:39:49,788] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:39:49,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/checkm_data
[2023-06-30 18:39:49,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:39:49,824] [INFO] Task started: CheckM
[2023-06-30 18:39:49,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900762145.1_SRS1170747_9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900762145.1_SRS1170747_9_genomic.fna/checkm_input GCA_900762145.1_SRS1170747_9_genomic.fna/checkm_result
[2023-06-30 18:40:11,020] [INFO] Task succeeded: CheckM
[2023-06-30 18:40:11,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:40:11,045] [INFO] ===== Completeness check finished =====
[2023-06-30 18:40:11,046] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:40:11,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900762145.1_SRS1170747_9_genomic.fna/markers.fasta)
[2023-06-30 18:40:11,047] [INFO] Task started: Blastn
[2023-06-30 18:40:11,047] [INFO] Running command: blastn -query GCA_900762145.1_SRS1170747_9_genomic.fna/markers.fasta -db /var/lib/cwl/stgd589f1d9-ffb5-42e0-9733-094cd2f19422/dqc_reference/reference_markers_gtdb.fasta -out GCA_900762145.1_SRS1170747_9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:40:11,932] [INFO] Task succeeded: Blastn
[2023-06-30 18:40:11,939] [INFO] Selected 24 target genomes.
[2023-06-30 18:40:11,939] [INFO] Target genome list was writen to GCA_900762145.1_SRS1170747_9_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:40:11,953] [INFO] Task started: fastANI
[2023-06-30 18:40:11,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgee2223c9-8994-403c-9c29-92bd811fcee5/GCA_900762145.1_SRS1170747_9_genomic.fna.gz --refList GCA_900762145.1_SRS1170747_9_genomic.fna/target_genomes_gtdb.txt --output GCA_900762145.1_SRS1170747_9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:40:22,760] [INFO] Task succeeded: fastANI
[2023-06-30 18:40:22,763] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 18:40:22,763] [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
--------------------------------------------------------------------------------
[2023-06-30 18:40:22,766] [INFO] GTDB search result was written to GCA_900762145.1_SRS1170747_9_genomic.fna/result_gtdb.tsv
[2023-06-30 18:40:22,767] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:40:22,769] [INFO] DFAST_QC result json was written to GCA_900762145.1_SRS1170747_9_genomic.fna/dqc_result.json
[2023-06-30 18:40:22,770] [INFO] DFAST_QC completed!
[2023-06-30 18:40:22,770] [INFO] Total running time: 0h0m52s