[2023-06-28 12:34:19,130] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:34:19,134] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:34:19,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference
[2023-06-28 12:34:21,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:34:21,262] [INFO] Task started: Prodigal
[2023-06-28 12:34:21,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg597f70f3-8422-4956-a1c5-6350c4c216c9/GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:34:24,492] [INFO] Task succeeded: Prodigal
[2023-06-28 12:34:24,493] [INFO] Task started: HMMsearch
[2023-06-28 12:34:24,493] [INFO] Running command: hmmsearch --tblout GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/reference_markers.hmm GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:34:24,699] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:34:24,702] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg597f70f3-8422-4956-a1c5-6350c4c216c9/GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 12:34:24,719] [INFO] Query marker FASTA was written to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 12:34:24,720] [INFO] Task started: Blastn
[2023-06-28 12:34:24,720] [INFO] Running command: blastn -query GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/reference_markers.fasta -out GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:25,868] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:25,882] [INFO] Selected 14 target genomes.
[2023-06-28 12:34:25,883] [INFO] Target genome list was writen to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 12:34:25,925] [INFO] Task started: fastANI
[2023-06-28 12:34:25,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg597f70f3-8422-4956-a1c5-6350c4c216c9/GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:34:31,566] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:31,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:34:31,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:34:31,570] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:34:31,570] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:34:31,570] [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 12:34:31,572] [INFO] DFAST Taxonomy check result was written to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 12:34:31,573] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:34:31,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:34:31,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/checkm_data
[2023-06-28 12:34:31,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:34:31,593] [INFO] Task started: CheckM
[2023-06-28 12:34:31,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 12:34:49,034] [INFO] Task succeeded: CheckM
[2023-06-28 12:34:49,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:34:49,057] [INFO] ===== Completeness check finished =====
[2023-06-28 12:34:49,057] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:34:49,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 12:34:49,058] [INFO] Task started: Blastn
[2023-06-28 12:34:49,058] [INFO] Running command: blastn -query GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg56201237-2802-45e4-9806-65f0135c0d3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:34:49,863] [INFO] Task succeeded: Blastn
[2023-06-28 12:34:49,867] [INFO] Selected 19 target genomes.
[2023-06-28 12:34:49,867] [INFO] Target genome list was writen to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:34:49,947] [INFO] Task started: fastANI
[2023-06-28 12:34:49,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg597f70f3-8422-4956-a1c5-6350c4c216c9/GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:34:54,188] [INFO] Task succeeded: fastANI
[2023-06-28 12:34:54,193] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 12:34:54,193] [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_003280225.1	s__AG-363-K07 sp003280225	77.285	55	201	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:34:54,196] [INFO] GTDB search result was written to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 12:34:54,196] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:34:54,199] [INFO] DFAST_QC result json was written to GCA_913041805.1_ERR599097_bin.46_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 12:34:54,199] [INFO] DFAST_QC completed!
[2023-06-28 12:34:54,199] [INFO] Total running time: 0h0m35s