[2023-06-30 05:04:01,122] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:04:01,125] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:04:01,125] [INFO] DQC Reference Directory: /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference
[2023-06-30 05:04:02,332] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:04:02,333] [INFO] Task started: Prodigal
[2023-06-30 05:04:02,333] [INFO] Running command: gunzip -c /var/lib/cwl/stg51c76047-2b05-4ff6-99d6-d951d0e86dc2/GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna.gz | prodigal -d GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/cds.fna -a GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:04:04,107] [INFO] Task succeeded: Prodigal
[2023-06-30 05:04:04,108] [INFO] Task started: HMMsearch
[2023-06-30 05:04:04,108] [INFO] Running command: hmmsearch --tblout GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/reference_markers.hmm GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:04:04,286] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:04:04,288] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg51c76047-2b05-4ff6-99d6-d951d0e86dc2/GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna.gz]
[2023-06-30 05:04:04,307] [INFO] Query marker FASTA was written to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/markers.fasta
[2023-06-30 05:04:04,308] [INFO] Task started: Blastn
[2023-06-30 05:04:04,308] [INFO] Running command: blastn -query GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/reference_markers.fasta -out GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:04,788] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:04,792] [INFO] Selected 10 target genomes.
[2023-06-30 05:04:04,793] [INFO] Target genome list was writen to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/target_genomes.txt
[2023-06-30 05:04:04,795] [INFO] Task started: fastANI
[2023-06-30 05:04:04,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c76047-2b05-4ff6-99d6-d951d0e86dc2/GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna.gz --refList GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/target_genomes.txt --output GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:04:11,110] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:11,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:04:11,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:04:11,114] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:04:11,114] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:04:11,114] [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 05:04:11,117] [INFO] DFAST Taxonomy check result was written to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/tc_result.tsv
[2023-06-30 05:04:11,117] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:04:11,118] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:04:11,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/checkm_data
[2023-06-30 05:04:11,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:04:11,136] [INFO] Task started: CheckM
[2023-06-30 05:04:11,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/checkm_input GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/checkm_result
[2023-06-30 05:04:24,536] [INFO] Task succeeded: CheckM
[2023-06-30 05:04:24,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:04:24,558] [INFO] ===== Completeness check finished =====
[2023-06-30 05:04:24,558] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:04:24,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/markers.fasta)
[2023-06-30 05:04:24,559] [INFO] Task started: Blastn
[2023-06-30 05:04:24,559] [INFO] Running command: blastn -query GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/markers.fasta -db /var/lib/cwl/stgc95cd4cf-c98a-41dd-9a3e-cc79bb7b0450/dqc_reference/reference_markers_gtdb.fasta -out GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:24,984] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:24,990] [INFO] Selected 12 target genomes.
[2023-06-30 05:04:24,990] [INFO] Target genome list was writen to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:04:24,994] [INFO] Task started: fastANI
[2023-06-30 05:04:24,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg51c76047-2b05-4ff6-99d6-d951d0e86dc2/GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna.gz --refList GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/target_genomes_gtdb.txt --output GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:04:27,292] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:27,295] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:04:27,295] [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 05:04:27,297] [INFO] GTDB search result was written to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/result_gtdb.tsv
[2023-06-30 05:04:27,297] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:04:27,299] [INFO] DFAST_QC result json was written to GCA_903822095.1_freshwater_MAG_---_LaPlata_bin-2074_genomic.fna/dqc_result.json
[2023-06-30 05:04:27,299] [INFO] DFAST_QC completed!
[2023-06-30 05:04:27,300] [INFO] Total running time: 0h0m26s