[2024-01-24 13:19:12,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:12,601] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:12,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference
[2024-01-24 13:19:13,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:13,908] [INFO] Task started: Prodigal
[2024-01-24 13:19:13,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg4376b08e-a377-4940-b2ba-6423fcd4f1c8/GCF_013133795.1_ASM1313379v1_genomic.fna.gz | prodigal -d GCF_013133795.1_ASM1313379v1_genomic.fna/cds.fna -a GCF_013133795.1_ASM1313379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:18,757] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:18,758] [INFO] Task started: HMMsearch
[2024-01-24 13:19:18,758] [INFO] Running command: hmmsearch --tblout GCF_013133795.1_ASM1313379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/reference_markers.hmm GCF_013133795.1_ASM1313379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:19,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:19,028] [INFO] Found 6/6 markers.
[2024-01-24 13:19:19,051] [INFO] Query marker FASTA was written to GCF_013133795.1_ASM1313379v1_genomic.fna/markers.fasta
[2024-01-24 13:19:19,052] [INFO] Task started: Blastn
[2024-01-24 13:19:19,052] [INFO] Running command: blastn -query GCF_013133795.1_ASM1313379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/reference_markers.fasta -out GCF_013133795.1_ASM1313379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:19,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:19,704] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:19,705] [INFO] Target genome list was writen to GCF_013133795.1_ASM1313379v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:19,717] [INFO] Task started: fastANI
[2024-01-24 13:19:19,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg4376b08e-a377-4940-b2ba-6423fcd4f1c8/GCF_013133795.1_ASM1313379v1_genomic.fna.gz --refList GCF_013133795.1_ASM1313379v1_genomic.fna/target_genomes.txt --output GCF_013133795.1_ASM1313379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:27,164] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:27,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:27,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:27,177] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:27,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:27,178] [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 suis	strain=3340-03	GCA_013133795.1	1631957	1631957	type	True	100.0	729	729	95	conclusive
Pelistega indica	strain=HM-7	GCA_000506865.1	1414851	1414851	type	True	78.5835	224	729	95	below_threshold
Pelistega europaea	strain=LMG10982	GCA_013133775.1	106147	106147	type	True	78.4874	226	729	95	below_threshold
Pelistega ratti	strain=NLN63	GCA_009833965.1	2652177	2652177	type	True	78.3596	195	729	95	below_threshold
Oligella ureolytica	strain=NCTC11997	GCA_900454285.1	90244	90244	type	True	76.5751	58	729	95	below_threshold
Oligella urethralis	strain=DSM 7531	GCA_000372065.1	90245	90245	type	True	76.2015	50	729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:27,179] [INFO] DFAST Taxonomy check result was written to GCF_013133795.1_ASM1313379v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:27,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:27,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:27,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/checkm_data
[2024-01-24 13:19:27,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:27,215] [INFO] Task started: CheckM
[2024-01-24 13:19:27,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013133795.1_ASM1313379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013133795.1_ASM1313379v1_genomic.fna/checkm_input GCF_013133795.1_ASM1313379v1_genomic.fna/checkm_result
[2024-01-24 13:19:48,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:48,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:48,608] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:48,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:48,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013133795.1_ASM1313379v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:48,610] [INFO] Task started: Blastn
[2024-01-24 13:19:48,610] [INFO] Running command: blastn -query GCF_013133795.1_ASM1313379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bb2de73-5188-48c1-88d3-976ccf3f73c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_013133795.1_ASM1313379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:49,711] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:49,714] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:49,715] [INFO] Target genome list was writen to GCF_013133795.1_ASM1313379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:49,816] [INFO] Task started: fastANI
[2024-01-24 13:19:49,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg4376b08e-a377-4940-b2ba-6423fcd4f1c8/GCF_013133795.1_ASM1313379v1_genomic.fna.gz --refList GCF_013133795.1_ASM1313379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013133795.1_ASM1313379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:55,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:55,683] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:55,684] [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_013133795.1	s__Pelistega suis	100.0	729	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000506865.1	s__Pelistega indica	78.6023	223	729	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	78.4874	226	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833965.1	s__Pelistega ratti	78.3596	195	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelistega	95.0	97.82	97.82	0.91	0.91	2	-
GCF_000373745.1	s__Oligella ureolytica	76.054	57	729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oligella	95.0	99.14	97.93	0.95	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,686] [INFO] GTDB search result was written to GCF_013133795.1_ASM1313379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:55,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:55,691] [INFO] DFAST_QC result json was written to GCF_013133795.1_ASM1313379v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:55,691] [INFO] DFAST_QC completed!
[2024-01-24 13:19:55,692] [INFO] Total running time: 0h0m43s