[2024-01-24 12:48:20,252] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,254] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference
[2024-01-24 12:48:21,515] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,516] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg682d7ed2-d59f-4c0a-88d7-bd45d94f9d0b/GCF_009833965.1_ASM983396v1_genomic.fna.gz | prodigal -d GCF_009833965.1_ASM983396v1_genomic.fna/cds.fna -a GCF_009833965.1_ASM983396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:25,999] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:25,999] [INFO] Task started: HMMsearch
[2024-01-24 12:48:25,999] [INFO] Running command: hmmsearch --tblout GCF_009833965.1_ASM983396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/reference_markers.hmm GCF_009833965.1_ASM983396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:26,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:26,248] [INFO] Found 6/6 markers.
[2024-01-24 12:48:26,274] [INFO] Query marker FASTA was written to GCF_009833965.1_ASM983396v1_genomic.fna/markers.fasta
[2024-01-24 12:48:26,274] [INFO] Task started: Blastn
[2024-01-24 12:48:26,274] [INFO] Running command: blastn -query GCF_009833965.1_ASM983396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/reference_markers.fasta -out GCF_009833965.1_ASM983396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:26,922] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:26,927] [INFO] Selected 22 target genomes.
[2024-01-24 12:48:26,928] [INFO] Target genome list was writen to GCF_009833965.1_ASM983396v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:26,950] [INFO] Task started: fastANI
[2024-01-24 12:48:26,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg682d7ed2-d59f-4c0a-88d7-bd45d94f9d0b/GCF_009833965.1_ASM983396v1_genomic.fna.gz --refList GCF_009833965.1_ASM983396v1_genomic.fna/target_genomes.txt --output GCF_009833965.1_ASM983396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:34,939] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:34,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:34,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:34,948] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:34,949] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:34,949] [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
Pelistega ratti	strain=NLN63	GCA_009833965.1	2652177	2652177	type	True	100.0	773	775	95	conclusive
Pelistega suis	strain=3340-03	GCA_013133795.1	1631957	1631957	type	True	78.4199	197	775	95	below_threshold
Pelistega indica	strain=HM-7	GCA_000506865.1	1414851	1414851	type	True	78.1817	185	775	95	below_threshold
Pelistega europaea	strain=LMG10982	GCA_013133775.1	106147	106147	type	True	78.1086	169	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:34,950] [INFO] DFAST Taxonomy check result was written to GCF_009833965.1_ASM983396v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:34,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:34,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:34,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/checkm_data
[2024-01-24 12:48:34,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:35,004] [INFO] Task started: CheckM
[2024-01-24 12:48:35,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009833965.1_ASM983396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009833965.1_ASM983396v1_genomic.fna/checkm_input GCF_009833965.1_ASM983396v1_genomic.fna/checkm_result
[2024-01-24 12:48:55,311] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:55,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:55,336] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:55,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:55,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009833965.1_ASM983396v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:55,338] [INFO] Task started: Blastn
[2024-01-24 12:48:55,338] [INFO] Running command: blastn -query GCF_009833965.1_ASM983396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg033c6b85-7919-49a9-85f4-e41032c80a70/dqc_reference/reference_markers_gtdb.fasta -out GCF_009833965.1_ASM983396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:56,335] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:56,339] [INFO] Selected 19 target genomes.
[2024-01-24 12:48:56,340] [INFO] Target genome list was writen to GCF_009833965.1_ASM983396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:56,375] [INFO] Task started: fastANI
[2024-01-24 12:48:56,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg682d7ed2-d59f-4c0a-88d7-bd45d94f9d0b/GCF_009833965.1_ASM983396v1_genomic.fna.gz --refList GCF_009833965.1_ASM983396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009833965.1_ASM983396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:03,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:03,608] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:03,608] [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_009833965.1	s__Pelistega ratti	100.0	774	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	97.82	97.82	0.91	0.91	2	conclusive
GCF_013133795.1	s__Pelistega suis	78.4199	197	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000506865.1	s__Pelistega indica	78.1817	185	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	99.45	98.91	0.95	0.92	3	-
GCF_013133775.1	s__Pelistega europaea	78.1085	169	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:03,610] [INFO] GTDB search result was written to GCF_009833965.1_ASM983396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:03,610] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:03,613] [INFO] DFAST_QC result json was written to GCF_009833965.1_ASM983396v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:03,614] [INFO] DFAST_QC completed!
[2024-01-24 12:49:03,614] [INFO] Total running time: 0h0m43s