[2023-06-08 09:53:44,441] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:53:44,447] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:53:44,447] [INFO] DQC Reference Directory: /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference
[2023-06-08 09:53:45,890] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:53:45,895] [INFO] Task started: Prodigal
[2023-06-08 09:53:45,895] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9eadb18-5053-48ef-a0ae-df72396bc72a/GCA_945889175.1_MH-21oct19-275_genomic.fna.gz | prodigal -d GCA_945889175.1_MH-21oct19-275_genomic.fna/cds.fna -a GCA_945889175.1_MH-21oct19-275_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:53:49,758] [INFO] Task succeeded: Prodigal
[2023-06-08 09:53:49,758] [INFO] Task started: HMMsearch
[2023-06-08 09:53:49,758] [INFO] Running command: hmmsearch --tblout GCA_945889175.1_MH-21oct19-275_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/reference_markers.hmm GCA_945889175.1_MH-21oct19-275_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:53:50,018] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:53:50,019] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf9eadb18-5053-48ef-a0ae-df72396bc72a/GCA_945889175.1_MH-21oct19-275_genomic.fna.gz]
[2023-06-08 09:53:50,039] [INFO] Query marker FASTA was written to GCA_945889175.1_MH-21oct19-275_genomic.fna/markers.fasta
[2023-06-08 09:53:50,040] [INFO] Task started: Blastn
[2023-06-08 09:53:50,040] [INFO] Running command: blastn -query GCA_945889175.1_MH-21oct19-275_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/reference_markers.fasta -out GCA_945889175.1_MH-21oct19-275_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:53:50,626] [INFO] Task succeeded: Blastn
[2023-06-08 09:53:50,630] [INFO] Selected 10 target genomes.
[2023-06-08 09:53:50,630] [INFO] Target genome list was writen to GCA_945889175.1_MH-21oct19-275_genomic.fna/target_genomes.txt
[2023-06-08 09:53:50,634] [INFO] Task started: fastANI
[2023-06-08 09:53:50,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9eadb18-5053-48ef-a0ae-df72396bc72a/GCA_945889175.1_MH-21oct19-275_genomic.fna.gz --refList GCA_945889175.1_MH-21oct19-275_genomic.fna/target_genomes.txt --output GCA_945889175.1_MH-21oct19-275_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:53:53,725] [INFO] Task succeeded: fastANI
[2023-06-08 09:53:53,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:53:53,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:53:53,734] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:53:53,734] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:53:53,734] [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
--------------------------------------------------------------------------------
[2023-06-08 09:53:53,741] [INFO] DFAST Taxonomy check result was written to GCA_945889175.1_MH-21oct19-275_genomic.fna/tc_result.tsv
[2023-06-08 09:53:53,742] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:53:53,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:53:53,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/checkm_data
[2023-06-08 09:53:53,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:53:53,786] [INFO] Task started: CheckM
[2023-06-08 09:53:53,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945889175.1_MH-21oct19-275_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945889175.1_MH-21oct19-275_genomic.fna/checkm_input GCA_945889175.1_MH-21oct19-275_genomic.fna/checkm_result
[2023-06-08 09:54:13,153] [INFO] Task succeeded: CheckM
[2023-06-08 09:54:13,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:54:13,181] [INFO] ===== Completeness check finished =====
[2023-06-08 09:54:13,182] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:54:13,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945889175.1_MH-21oct19-275_genomic.fna/markers.fasta)
[2023-06-08 09:54:13,182] [INFO] Task started: Blastn
[2023-06-08 09:54:13,183] [INFO] Running command: blastn -query GCA_945889175.1_MH-21oct19-275_genomic.fna/markers.fasta -db /var/lib/cwl/stg75c43678-877e-4443-a501-49c493860263/dqc_reference/reference_markers_gtdb.fasta -out GCA_945889175.1_MH-21oct19-275_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:13,940] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:13,944] [INFO] Selected 16 target genomes.
[2023-06-08 09:54:13,944] [INFO] Target genome list was writen to GCA_945889175.1_MH-21oct19-275_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:54:14,012] [INFO] Task started: fastANI
[2023-06-08 09:54:14,012] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9eadb18-5053-48ef-a0ae-df72396bc72a/GCA_945889175.1_MH-21oct19-275_genomic.fna.gz --refList GCA_945889175.1_MH-21oct19-275_genomic.fna/target_genomes_gtdb.txt --output GCA_945889175.1_MH-21oct19-275_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:54:17,707] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:17,710] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:54:17,710] [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
--------------------------------------------------------------------------------
[2023-06-08 09:54:17,712] [INFO] GTDB search result was written to GCA_945889175.1_MH-21oct19-275_genomic.fna/result_gtdb.tsv
[2023-06-08 09:54:17,713] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:54:17,716] [INFO] DFAST_QC result json was written to GCA_945889175.1_MH-21oct19-275_genomic.fna/dqc_result.json
[2023-06-08 09:54:17,717] [INFO] DFAST_QC completed!
[2023-06-08 09:54:17,717] [INFO] Total running time: 0h0m33s