[2023-06-28 12:49:49,960] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:49:49,962] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:49:49,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference
[2023-06-28 12:49:51,443] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:49:51,444] [INFO] Task started: Prodigal
[2023-06-28 12:49:51,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d079bda-21f6-4b48-b8db-4df21158397a/GCA_027310375.1_ASM2731037v1_genomic.fna.gz | prodigal -d GCA_027310375.1_ASM2731037v1_genomic.fna/cds.fna -a GCA_027310375.1_ASM2731037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:49:53,520] [INFO] Task succeeded: Prodigal
[2023-06-28 12:49:53,520] [INFO] Task started: HMMsearch
[2023-06-28 12:49:53,520] [INFO] Running command: hmmsearch --tblout GCA_027310375.1_ASM2731037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/reference_markers.hmm GCA_027310375.1_ASM2731037v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:49:53,735] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:49:53,737] [INFO] Found 6/6 markers.
[2023-06-28 12:49:53,753] [INFO] Query marker FASTA was written to GCA_027310375.1_ASM2731037v1_genomic.fna/markers.fasta
[2023-06-28 12:49:53,753] [INFO] Task started: Blastn
[2023-06-28 12:49:53,754] [INFO] Running command: blastn -query GCA_027310375.1_ASM2731037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/reference_markers.fasta -out GCA_027310375.1_ASM2731037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:49:55,985] [INFO] Task succeeded: Blastn
[2023-06-28 12:49:55,990] [INFO] Selected 15 target genomes.
[2023-06-28 12:49:55,991] [INFO] Target genome list was writen to GCA_027310375.1_ASM2731037v1_genomic.fna/target_genomes.txt
[2023-06-28 12:49:55,995] [INFO] Task started: fastANI
[2023-06-28 12:49:55,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d079bda-21f6-4b48-b8db-4df21158397a/GCA_027310375.1_ASM2731037v1_genomic.fna.gz --refList GCA_027310375.1_ASM2731037v1_genomic.fna/target_genomes.txt --output GCA_027310375.1_ASM2731037v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:50:05,164] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:05,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:50:05,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:50:05,167] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:50:05,167] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:50:05,167] [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 12:50:05,169] [INFO] DFAST Taxonomy check result was written to GCA_027310375.1_ASM2731037v1_genomic.fna/tc_result.tsv
[2023-06-28 12:50:05,169] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:50:05,169] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:50:05,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/checkm_data
[2023-06-28 12:50:05,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:50:05,188] [INFO] Task started: CheckM
[2023-06-28 12:50:05,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310375.1_ASM2731037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310375.1_ASM2731037v1_genomic.fna/checkm_input GCA_027310375.1_ASM2731037v1_genomic.fna/checkm_result
[2023-06-28 12:50:19,638] [INFO] Task succeeded: CheckM
[2023-06-28 12:50:19,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:50:19,658] [INFO] ===== Completeness check finished =====
[2023-06-28 12:50:19,659] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:50:19,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310375.1_ASM2731037v1_genomic.fna/markers.fasta)
[2023-06-28 12:50:19,659] [INFO] Task started: Blastn
[2023-06-28 12:50:19,660] [INFO] Running command: blastn -query GCA_027310375.1_ASM2731037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47427fdf-1373-445f-976f-ba5db846e9e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310375.1_ASM2731037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:50:20,456] [INFO] Task succeeded: Blastn
[2023-06-28 12:50:20,461] [INFO] Selected 17 target genomes.
[2023-06-28 12:50:20,462] [INFO] Target genome list was writen to GCA_027310375.1_ASM2731037v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:50:20,474] [INFO] Task started: fastANI
[2023-06-28 12:50:20,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d079bda-21f6-4b48-b8db-4df21158397a/GCA_027310375.1_ASM2731037v1_genomic.fna.gz --refList GCA_027310375.1_ASM2731037v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310375.1_ASM2731037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:50:24,080] [INFO] Task succeeded: fastANI
[2023-06-28 12:50:24,087] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:50:24,087] [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_004100325.1	s__UBA6175 sp004100325	99.9976	261	263	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA6175	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002429245.1	s__UBA6175 sp002429245	78.0984	87	263	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__UBA1547;g__UBA6175	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:50:24,090] [INFO] GTDB search result was written to GCA_027310375.1_ASM2731037v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:50:24,091] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:50:24,093] [INFO] DFAST_QC result json was written to GCA_027310375.1_ASM2731037v1_genomic.fna/dqc_result.json
[2023-06-28 12:50:24,093] [INFO] DFAST_QC completed!
[2023-06-28 12:50:24,094] [INFO] Total running time: 0h0m34s