[2023-06-19 03:53:19,805] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:53:19,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:53:19,809] [INFO] DQC Reference Directory: /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference
[2023-06-19 03:53:21,118] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:53:21,119] [INFO] Task started: Prodigal
[2023-06-19 03:53:21,119] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa303286-423b-46cd-b938-e6015bea274f/GCA_018377045.1_ASM1837704v1_genomic.fna.gz | prodigal -d GCA_018377045.1_ASM1837704v1_genomic.fna/cds.fna -a GCA_018377045.1_ASM1837704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:53:23,482] [INFO] Task succeeded: Prodigal
[2023-06-19 03:53:23,482] [INFO] Task started: HMMsearch
[2023-06-19 03:53:23,482] [INFO] Running command: hmmsearch --tblout GCA_018377045.1_ASM1837704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/reference_markers.hmm GCA_018377045.1_ASM1837704v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:53:23,723] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:53:23,725] [INFO] Found 6/6 markers.
[2023-06-19 03:53:23,749] [INFO] Query marker FASTA was written to GCA_018377045.1_ASM1837704v1_genomic.fna/markers.fasta
[2023-06-19 03:53:23,750] [INFO] Task started: Blastn
[2023-06-19 03:53:23,750] [INFO] Running command: blastn -query GCA_018377045.1_ASM1837704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/reference_markers.fasta -out GCA_018377045.1_ASM1837704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:26,707] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:26,711] [INFO] Selected 17 target genomes.
[2023-06-19 03:53:26,711] [INFO] Target genome list was writen to GCA_018377045.1_ASM1837704v1_genomic.fna/target_genomes.txt
[2023-06-19 03:53:26,727] [INFO] Task started: fastANI
[2023-06-19 03:53:26,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa303286-423b-46cd-b938-e6015bea274f/GCA_018377045.1_ASM1837704v1_genomic.fna.gz --refList GCA_018377045.1_ASM1837704v1_genomic.fna/target_genomes.txt --output GCA_018377045.1_ASM1837704v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:53:35,210] [INFO] Task succeeded: fastANI
[2023-06-19 03:53:35,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:53:35,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:53:35,214] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:53:35,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:53:35,215] [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
Allisonella histaminiformans	strain=DSM 15230	GCA_900103425.1	209880	209880	type	True	78.7361	64	400	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:53:35,217] [INFO] DFAST Taxonomy check result was written to GCA_018377045.1_ASM1837704v1_genomic.fna/tc_result.tsv
[2023-06-19 03:53:35,217] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:53:35,217] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:53:35,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/checkm_data
[2023-06-19 03:53:35,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:53:35,234] [INFO] Task started: CheckM
[2023-06-19 03:53:35,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018377045.1_ASM1837704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018377045.1_ASM1837704v1_genomic.fna/checkm_input GCA_018377045.1_ASM1837704v1_genomic.fna/checkm_result
[2023-06-19 03:53:51,902] [INFO] Task succeeded: CheckM
[2023-06-19 03:53:51,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 03:53:51,923] [INFO] ===== Completeness check finished =====
[2023-06-19 03:53:51,923] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:53:51,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018377045.1_ASM1837704v1_genomic.fna/markers.fasta)
[2023-06-19 03:53:51,924] [INFO] Task started: Blastn
[2023-06-19 03:53:51,924] [INFO] Running command: blastn -query GCA_018377045.1_ASM1837704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab650d33-00d5-41f5-b99e-0214cc4ee004/dqc_reference/reference_markers_gtdb.fasta -out GCA_018377045.1_ASM1837704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:53:52,764] [INFO] Task succeeded: Blastn
[2023-06-19 03:53:52,770] [INFO] Selected 22 target genomes.
[2023-06-19 03:53:52,770] [INFO] Target genome list was writen to GCA_018377045.1_ASM1837704v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:53:52,779] [INFO] Task started: fastANI
[2023-06-19 03:53:52,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa303286-423b-46cd-b938-e6015bea274f/GCA_018377045.1_ASM1837704v1_genomic.fna.gz --refList GCA_018377045.1_ASM1837704v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018377045.1_ASM1837704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:54:00,958] [INFO] Task succeeded: fastANI
[2023-06-19 03:54:00,962] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 03:54:00,963] [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
GCF_001717505.1	s__Allisonella pneumosintes	99.5662	387	400	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Allisonella	95.0	99.48	99.38	0.97	0.94	6	conclusive
GCF_900103425.1	s__Allisonella histaminiformans	78.7361	64	400	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Allisonella	95.0	98.29	97.91	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-19 03:54:00,965] [INFO] GTDB search result was written to GCA_018377045.1_ASM1837704v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:54:00,965] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:54:00,968] [INFO] DFAST_QC result json was written to GCA_018377045.1_ASM1837704v1_genomic.fna/dqc_result.json
[2023-06-19 03:54:00,968] [INFO] DFAST_QC completed!
[2023-06-19 03:54:00,968] [INFO] Total running time: 0h0m41s