[2023-06-16 23:36:46,281] [INFO] DFAST_QC pipeline started.
[2023-06-16 23:36:46,283] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 23:36:46,283] [INFO] DQC Reference Directory: /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference
[2023-06-16 23:36:48,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 23:36:48,563] [INFO] Task started: Prodigal
[2023-06-16 23:36:48,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg808bd28a-0235-4064-86b7-9a7047667aa7/GCA_013333815.2_ASM1333381v2_genomic.fna.gz | prodigal -d GCA_013333815.2_ASM1333381v2_genomic.fna/cds.fna -a GCA_013333815.2_ASM1333381v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 23:36:50,060] [INFO] Task succeeded: Prodigal
[2023-06-16 23:36:50,061] [INFO] Task started: HMMsearch
[2023-06-16 23:36:50,061] [INFO] Running command: hmmsearch --tblout GCA_013333815.2_ASM1333381v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/reference_markers.hmm GCA_013333815.2_ASM1333381v2_genomic.fna/protein.faa > /dev/null
[2023-06-16 23:36:50,231] [INFO] Task succeeded: HMMsearch
[2023-06-16 23:36:50,233] [INFO] Found 6/6 markers.
[2023-06-16 23:36:50,251] [INFO] Query marker FASTA was written to GCA_013333815.2_ASM1333381v2_genomic.fna/markers.fasta
[2023-06-16 23:36:50,252] [INFO] Task started: Blastn
[2023-06-16 23:36:50,252] [INFO] Running command: blastn -query GCA_013333815.2_ASM1333381v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/reference_markers.fasta -out GCA_013333815.2_ASM1333381v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:36:52,925] [INFO] Task succeeded: Blastn
[2023-06-16 23:36:52,929] [INFO] Selected 11 target genomes.
[2023-06-16 23:36:52,929] [INFO] Target genome list was writen to GCA_013333815.2_ASM1333381v2_genomic.fna/target_genomes.txt
[2023-06-16 23:36:52,933] [INFO] Task started: fastANI
[2023-06-16 23:36:52,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg808bd28a-0235-4064-86b7-9a7047667aa7/GCA_013333815.2_ASM1333381v2_genomic.fna.gz --refList GCA_013333815.2_ASM1333381v2_genomic.fna/target_genomes.txt --output GCA_013333815.2_ASM1333381v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 23:36:59,899] [INFO] Task succeeded: fastANI
[2023-06-16 23:36:59,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 23:36:59,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 23:36:59,902] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 23:36:59,903] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 23:36:59,903] [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
--------------------------------------------------------------------------------
[2023-06-16 23:36:59,906] [INFO] DFAST Taxonomy check result was written to GCA_013333815.2_ASM1333381v2_genomic.fna/tc_result.tsv
[2023-06-16 23:36:59,907] [INFO] ===== Taxonomy check completed =====
[2023-06-16 23:36:59,907] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 23:36:59,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/checkm_data
[2023-06-16 23:36:59,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 23:36:59,928] [INFO] Task started: CheckM
[2023-06-16 23:36:59,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013333815.2_ASM1333381v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013333815.2_ASM1333381v2_genomic.fna/checkm_input GCA_013333815.2_ASM1333381v2_genomic.fna/checkm_result
[2023-06-16 23:37:12,874] [INFO] Task succeeded: CheckM
[2023-06-16 23:37:12,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 23:37:12,897] [INFO] ===== Completeness check finished =====
[2023-06-16 23:37:12,897] [INFO] ===== Start GTDB Search =====
[2023-06-16 23:37:12,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013333815.2_ASM1333381v2_genomic.fna/markers.fasta)
[2023-06-16 23:37:12,898] [INFO] Task started: Blastn
[2023-06-16 23:37:12,898] [INFO] Running command: blastn -query GCA_013333815.2_ASM1333381v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge7cafd91-619c-43f1-bca8-66e34cca0e67/dqc_reference/reference_markers_gtdb.fasta -out GCA_013333815.2_ASM1333381v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 23:37:13,690] [INFO] Task succeeded: Blastn
[2023-06-16 23:37:13,695] [INFO] Selected 19 target genomes.
[2023-06-16 23:37:13,696] [INFO] Target genome list was writen to GCA_013333815.2_ASM1333381v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 23:37:13,717] [INFO] Task started: fastANI
[2023-06-16 23:37:13,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg808bd28a-0235-4064-86b7-9a7047667aa7/GCA_013333815.2_ASM1333381v2_genomic.fna.gz --refList GCA_013333815.2_ASM1333381v2_genomic.fna/target_genomes_gtdb.txt --output GCA_013333815.2_ASM1333381v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 23:37:18,590] [INFO] Task succeeded: fastANI
[2023-06-16 23:37:18,592] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 23:37:18,593] [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_007845485.1	s__SDRW01 sp007845485	97.3978	216	248	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA10027;g__SDRW01	95.0	97.36	97.09	0.86	0.73	8	conclusive
--------------------------------------------------------------------------------
[2023-06-16 23:37:18,595] [INFO] GTDB search result was written to GCA_013333815.2_ASM1333381v2_genomic.fna/result_gtdb.tsv
[2023-06-16 23:37:18,596] [INFO] ===== GTDB Search completed =====
[2023-06-16 23:37:18,598] [INFO] DFAST_QC result json was written to GCA_013333815.2_ASM1333381v2_genomic.fna/dqc_result.json
[2023-06-16 23:37:18,599] [INFO] DFAST_QC completed!
[2023-06-16 23:37:18,599] [INFO] Total running time: 0h0m32s