[2023-06-17 14:17:56,161] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:17:56,163] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:17:56,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference
[2023-06-17 14:17:57,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:17:57,473] [INFO] Task started: Prodigal
[2023-06-17 14:17:57,473] [INFO] Running command: gunzip -c /var/lib/cwl/stg33dba746-cca1-41be-86a3-7b24dee00494/GCA_028708885.1_ASM2870888v1_genomic.fna.gz | prodigal -d GCA_028708885.1_ASM2870888v1_genomic.fna/cds.fna -a GCA_028708885.1_ASM2870888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:18:08,550] [INFO] Task succeeded: Prodigal
[2023-06-17 14:18:08,551] [INFO] Task started: HMMsearch
[2023-06-17 14:18:08,551] [INFO] Running command: hmmsearch --tblout GCA_028708885.1_ASM2870888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/reference_markers.hmm GCA_028708885.1_ASM2870888v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:18:08,825] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:18:08,827] [INFO] Found 6/6 markers.
[2023-06-17 14:18:08,855] [INFO] Query marker FASTA was written to GCA_028708885.1_ASM2870888v1_genomic.fna/markers.fasta
[2023-06-17 14:18:08,856] [INFO] Task started: Blastn
[2023-06-17 14:18:08,856] [INFO] Running command: blastn -query GCA_028708885.1_ASM2870888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/reference_markers.fasta -out GCA_028708885.1_ASM2870888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:18:09,446] [INFO] Task succeeded: Blastn
[2023-06-17 14:18:09,452] [INFO] Selected 25 target genomes.
[2023-06-17 14:18:09,453] [INFO] Target genome list was writen to GCA_028708885.1_ASM2870888v1_genomic.fna/target_genomes.txt
[2023-06-17 14:18:09,461] [INFO] Task started: fastANI
[2023-06-17 14:18:09,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dba746-cca1-41be-86a3-7b24dee00494/GCA_028708885.1_ASM2870888v1_genomic.fna.gz --refList GCA_028708885.1_ASM2870888v1_genomic.fna/target_genomes.txt --output GCA_028708885.1_ASM2870888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:18:23,960] [INFO] Task succeeded: fastANI
[2023-06-17 14:18:23,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:18:23,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:18:23,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:18:23,964] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 14:18:23,964] [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
--------------------------------------------------------------------------------
[2023-06-17 14:18:23,966] [INFO] DFAST Taxonomy check result was written to GCA_028708885.1_ASM2870888v1_genomic.fna/tc_result.tsv
[2023-06-17 14:18:23,967] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:18:23,967] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:18:23,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/checkm_data
[2023-06-17 14:18:23,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:18:24,004] [INFO] Task started: CheckM
[2023-06-17 14:18:24,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708885.1_ASM2870888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708885.1_ASM2870888v1_genomic.fna/checkm_input GCA_028708885.1_ASM2870888v1_genomic.fna/checkm_result
[2023-06-17 14:19:01,952] [INFO] Task succeeded: CheckM
[2023-06-17 14:19:01,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:19:01,973] [INFO] ===== Completeness check finished =====
[2023-06-17 14:19:01,974] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:19:01,974] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708885.1_ASM2870888v1_genomic.fna/markers.fasta)
[2023-06-17 14:19:01,975] [INFO] Task started: Blastn
[2023-06-17 14:19:01,975] [INFO] Running command: blastn -query GCA_028708885.1_ASM2870888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa9cdfb6-23e1-4d54-bed1-1383d796f22e/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708885.1_ASM2870888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:19:02,730] [INFO] Task succeeded: Blastn
[2023-06-17 14:19:02,736] [INFO] Selected 34 target genomes.
[2023-06-17 14:19:02,737] [INFO] Target genome list was writen to GCA_028708885.1_ASM2870888v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:19:02,767] [INFO] Task started: fastANI
[2023-06-17 14:19:02,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg33dba746-cca1-41be-86a3-7b24dee00494/GCA_028708885.1_ASM2870888v1_genomic.fna.gz --refList GCA_028708885.1_ASM2870888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708885.1_ASM2870888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:19:16,438] [INFO] Task succeeded: fastANI
[2023-06-17 14:19:16,441] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:19:16,441] [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
--------------------------------------------------------------------------------
[2023-06-17 14:19:16,444] [INFO] GTDB search result was written to GCA_028708885.1_ASM2870888v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:19:16,445] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:19:16,448] [INFO] DFAST_QC result json was written to GCA_028708885.1_ASM2870888v1_genomic.fna/dqc_result.json
[2023-06-17 14:19:16,449] [INFO] DFAST_QC completed!
[2023-06-17 14:19:16,449] [INFO] Total running time: 0h1m20s