[2023-06-28 12:49:39,722] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:39,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:39,725] [INFO] DQC Reference Directory: /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference
[2023-06-28 12:49:41,122] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:41,123] [INFO] Task started: Prodigal
[2023-06-28 12:49:41,123] [INFO] Running command: gunzip -c /var/lib/cwl/stg192dcd18-e40c-4dc1-b142-39bbf4ac3617/GCA_020057665.1_ASM2005766v1_genomic.fna.gz | prodigal -d GCA_020057665.1_ASM2005766v1_genomic.fna/cds.fna -a GCA_020057665.1_ASM2005766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:43,224] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:43,225] [INFO] Task started: HMMsearch
[2023-06-28 12:49:43,225] [INFO] Running command: hmmsearch --tblout GCA_020057665.1_ASM2005766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/reference_markers.hmm GCA_020057665.1_ASM2005766v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:43,439] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:43,440] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg192dcd18-e40c-4dc1-b142-39bbf4ac3617/GCA_020057665.1_ASM2005766v1_genomic.fna.gz]
[2023-06-28 12:49:43,458] [INFO] Query marker FASTA was written to GCA_020057665.1_ASM2005766v1_genomic.fna/markers.fasta
[2023-06-28 12:49:43,459] [INFO] Task started: Blastn
[2023-06-28 12:49:43,459] [INFO] Running command: blastn -query GCA_020057665.1_ASM2005766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/reference_markers.fasta -out GCA_020057665.1_ASM2005766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:43,980] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:43,985] [INFO] Selected 5 target genomes.
[2023-06-28 12:49:43,985] [INFO] Target genome list was writen to GCA_020057665.1_ASM2005766v1_genomic.fna/target_genomes.txt
[2023-06-28 12:49:44,020] [INFO] Task started: fastANI
[2023-06-28 12:49:44,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg192dcd18-e40c-4dc1-b142-39bbf4ac3617/GCA_020057665.1_ASM2005766v1_genomic.fna.gz --refList GCA_020057665.1_ASM2005766v1_genomic.fna/target_genomes.txt --output GCA_020057665.1_ASM2005766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:49:45,655] [INFO] Task succeeded: fastANI
[2023-06-28 12:49:45,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:49:45,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:49:45,658] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:49:45,658] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:49:45,658] [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
--------------------------------------------------------------------------------
[2023-06-28 12:49:45,660] [INFO] DFAST Taxonomy check result was written to GCA_020057665.1_ASM2005766v1_genomic.fna/tc_result.tsv
[2023-06-28 12:49:45,661] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:49:45,661] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:49:45,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/checkm_data
[2023-06-28 12:49:45,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:49:45,684] [INFO] Task started: CheckM
[2023-06-28 12:49:45,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020057665.1_ASM2005766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020057665.1_ASM2005766v1_genomic.fna/checkm_input GCA_020057665.1_ASM2005766v1_genomic.fna/checkm_result
[2023-06-28 12:50:01,326] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:01,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.87%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:01,359] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:01,359] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:01,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020057665.1_ASM2005766v1_genomic.fna/markers.fasta)
[2023-06-28 12:50:01,360] [INFO] Task started: Blastn
[2023-06-28 12:50:01,360] [INFO] Running command: blastn -query GCA_020057665.1_ASM2005766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged7189d0-fe16-47b9-8745-1a8f157d1d72/dqc_reference/reference_markers_gtdb.fasta -out GCA_020057665.1_ASM2005766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:01,890] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:01,895] [INFO] Selected 8 target genomes.
[2023-06-28 12:50:01,895] [INFO] Target genome list was writen to GCA_020057665.1_ASM2005766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:01,901] [INFO] Task started: fastANI
[2023-06-28 12:50:01,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg192dcd18-e40c-4dc1-b142-39bbf4ac3617/GCA_020057665.1_ASM2005766v1_genomic.fna.gz --refList GCA_020057665.1_ASM2005766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020057665.1_ASM2005766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:05,801] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:05,812] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:50:05,813] [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_016215115.1	s__SURF-23 sp016215115	88.8167	158	270	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599505.1	s__SURF-23 sp003599505	79.6554	54	270	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213945.1	s__SURF-23 sp016213945	78.6733	74	270	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214845.1	s__SURF-23 sp016214845	78.3032	70	270	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__UBA6902;f__UBA6902;g__SURF-23	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:05,818] [INFO] GTDB search result was written to GCA_020057665.1_ASM2005766v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:05,819] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:05,823] [INFO] DFAST_QC result json was written to GCA_020057665.1_ASM2005766v1_genomic.fna/dqc_result.json
[2023-06-28 12:50:05,823] [INFO] DFAST_QC completed!
[2023-06-28 12:50:05,823] [INFO] Total running time: 0h0m26s