[2023-06-29 22:41:15,278] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:41:15,281] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:41:15,281] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference
[2023-06-29 22:41:16,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:41:16,648] [INFO] Task started: Prodigal
[2023-06-29 22:41:16,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg483cbc43-9ebe-4a53-9fdf-3f66665c2f7d/GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna.gz | prodigal -d GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/cds.fna -a GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:41:24,446] [INFO] Task succeeded: Prodigal
[2023-06-29 22:41:24,446] [INFO] Task started: HMMsearch
[2023-06-29 22:41:24,447] [INFO] Running command: hmmsearch --tblout GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/reference_markers.hmm GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:41:24,732] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:41:24,734] [INFO] Found 6/6 markers.
[2023-06-29 22:41:24,775] [INFO] Query marker FASTA was written to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/markers.fasta
[2023-06-29 22:41:24,776] [INFO] Task started: Blastn
[2023-06-29 22:41:24,776] [INFO] Running command: blastn -query GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/reference_markers.fasta -out GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:41:25,387] [INFO] Task succeeded: Blastn
[2023-06-29 22:41:25,392] [INFO] Selected 20 target genomes.
[2023-06-29 22:41:25,393] [INFO] Target genome list was writen to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/target_genomes.txt
[2023-06-29 22:41:25,396] [INFO] Task started: fastANI
[2023-06-29 22:41:25,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg483cbc43-9ebe-4a53-9fdf-3f66665c2f7d/GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna.gz --refList GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/target_genomes.txt --output GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:41:39,142] [INFO] Task succeeded: fastANI
[2023-06-29 22:41:39,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:41:39,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:41:39,145] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:41:39,145] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:41:39,145] [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
--------------------------------------------------------------------------------
[2023-06-29 22:41:39,147] [INFO] DFAST Taxonomy check result was written to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/tc_result.tsv
[2023-06-29 22:41:39,148] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:41:39,148] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:41:39,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/checkm_data
[2023-06-29 22:41:39,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:41:39,189] [INFO] Task started: CheckM
[2023-06-29 22:41:39,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/checkm_input GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/checkm_result
[2023-06-29 22:42:07,403] [INFO] Task succeeded: CheckM
[2023-06-29 22:42:07,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.91%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:42:07,428] [INFO] ===== Completeness check finished =====
[2023-06-29 22:42:07,428] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:42:07,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/markers.fasta)
[2023-06-29 22:42:07,429] [INFO] Task started: Blastn
[2023-06-29 22:42:07,429] [INFO] Running command: blastn -query GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa1fe150-5058-4669-8662-2c386a3aad62/dqc_reference/reference_markers_gtdb.fasta -out GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:42:08,265] [INFO] Task succeeded: Blastn
[2023-06-29 22:42:08,270] [INFO] Selected 25 target genomes.
[2023-06-29 22:42:08,270] [INFO] Target genome list was writen to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:42:08,299] [INFO] Task started: fastANI
[2023-06-29 22:42:08,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg483cbc43-9ebe-4a53-9fdf-3f66665c2f7d/GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna.gz --refList GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/target_genomes_gtdb.txt --output GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:42:21,767] [INFO] Task succeeded: fastANI
[2023-06-29 22:42:21,772] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 22:42:21,772] [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_002298885.1	s__UBA700 sp002298885	76.1885	58	421	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:42:21,774] [INFO] GTDB search result was written to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/result_gtdb.tsv
[2023-06-29 22:42:21,775] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:42:21,778] [INFO] DFAST_QC result json was written to GCA_903894255.1_freshwater_MAG_---_LaPlata-15m-a_bin-134_genomic.fna/dqc_result.json
[2023-06-29 22:42:21,778] [INFO] DFAST_QC completed!
[2023-06-29 22:42:21,778] [INFO] Total running time: 0h1m7s