[2023-06-13 08:07:28,655] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:07:28,657] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:07:28,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference
[2023-06-13 08:07:30,003] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:07:30,004] [INFO] Task started: Prodigal
[2023-06-13 08:07:30,004] [INFO] Running command: gunzip -c /var/lib/cwl/stga4dee30d-dd42-4ea9-bbed-204e3b9b56c0/GCA_022707005.1_ASM2270700v1_genomic.fna.gz | prodigal -d GCA_022707005.1_ASM2270700v1_genomic.fna/cds.fna -a GCA_022707005.1_ASM2270700v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:07:33,488] [INFO] Task succeeded: Prodigal
[2023-06-13 08:07:33,488] [INFO] Task started: HMMsearch
[2023-06-13 08:07:33,489] [INFO] Running command: hmmsearch --tblout GCA_022707005.1_ASM2270700v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/reference_markers.hmm GCA_022707005.1_ASM2270700v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:07:33,750] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:07:33,752] [INFO] Found 6/6 markers.
[2023-06-13 08:07:33,774] [INFO] Query marker FASTA was written to GCA_022707005.1_ASM2270700v1_genomic.fna/markers.fasta
[2023-06-13 08:07:33,774] [INFO] Task started: Blastn
[2023-06-13 08:07:33,774] [INFO] Running command: blastn -query GCA_022707005.1_ASM2270700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/reference_markers.fasta -out GCA_022707005.1_ASM2270700v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:07:34,398] [INFO] Task succeeded: Blastn
[2023-06-13 08:07:34,402] [INFO] Selected 12 target genomes.
[2023-06-13 08:07:34,402] [INFO] Target genome list was writen to GCA_022707005.1_ASM2270700v1_genomic.fna/target_genomes.txt
[2023-06-13 08:07:34,406] [INFO] Task started: fastANI
[2023-06-13 08:07:34,406] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dee30d-dd42-4ea9-bbed-204e3b9b56c0/GCA_022707005.1_ASM2270700v1_genomic.fna.gz --refList GCA_022707005.1_ASM2270700v1_genomic.fna/target_genomes.txt --output GCA_022707005.1_ASM2270700v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:07:40,800] [INFO] Task succeeded: fastANI
[2023-06-13 08:07:40,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:07:40,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:07:40,802] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:07:40,802] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 08:07:40,802] [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 08:07:40,804] [INFO] DFAST Taxonomy check result was written to GCA_022707005.1_ASM2270700v1_genomic.fna/tc_result.tsv
[2023-06-13 08:07:40,805] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:07:40,805] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:07:40,805] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/checkm_data
[2023-06-13 08:07:40,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:07:40,832] [INFO] Task started: CheckM
[2023-06-13 08:07:40,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022707005.1_ASM2270700v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022707005.1_ASM2270700v1_genomic.fna/checkm_input GCA_022707005.1_ASM2270700v1_genomic.fna/checkm_result
[2023-06-13 08:07:59,039] [INFO] Task succeeded: CheckM
[2023-06-13 08:07:59,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:07:59,061] [INFO] ===== Completeness check finished =====
[2023-06-13 08:07:59,062] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:07:59,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022707005.1_ASM2270700v1_genomic.fna/markers.fasta)
[2023-06-13 08:07:59,063] [INFO] Task started: Blastn
[2023-06-13 08:07:59,063] [INFO] Running command: blastn -query GCA_022707005.1_ASM2270700v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10d1f43f-b005-451c-82a9-6e05d4ff6d08/dqc_reference/reference_markers_gtdb.fasta -out GCA_022707005.1_ASM2270700v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:08:00,070] [INFO] Task succeeded: Blastn
[2023-06-13 08:08:00,074] [INFO] Selected 21 target genomes.
[2023-06-13 08:08:00,074] [INFO] Target genome list was writen to GCA_022707005.1_ASM2270700v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:08:00,105] [INFO] Task started: fastANI
[2023-06-13 08:08:00,105] [INFO] Running command: fastANI --query /var/lib/cwl/stga4dee30d-dd42-4ea9-bbed-204e3b9b56c0/GCA_022707005.1_ASM2270700v1_genomic.fna.gz --refList GCA_022707005.1_ASM2270700v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022707005.1_ASM2270700v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:08:08,045] [INFO] Task succeeded: fastANI
[2023-06-13 08:08:08,047] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 08:08:08,048] [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
--------------------------------------------------------------------------------
[2023-06-13 08:08:08,050] [INFO] GTDB search result was written to GCA_022707005.1_ASM2270700v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:08:08,051] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:08:08,053] [INFO] DFAST_QC result json was written to GCA_022707005.1_ASM2270700v1_genomic.fna/dqc_result.json
[2023-06-13 08:08:08,054] [INFO] DFAST_QC completed!
[2023-06-13 08:08:08,054] [INFO] Total running time: 0h0m39s