[2024-01-25 19:38:50,567] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:50,569] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:50,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference
[2024-01-25 19:38:51,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:51,739] [INFO] Task started: Prodigal
[2024-01-25 19:38:51,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg148b37df-1a90-483c-b65d-c2e473775d56/GCF_014837015.1_ASM1483701v1_genomic.fna.gz | prodigal -d GCF_014837015.1_ASM1483701v1_genomic.fna/cds.fna -a GCF_014837015.1_ASM1483701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:58,525] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:58,525] [INFO] Task started: HMMsearch
[2024-01-25 19:38:58,525] [INFO] Running command: hmmsearch --tblout GCF_014837015.1_ASM1483701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/reference_markers.hmm GCF_014837015.1_ASM1483701v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:58,752] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:58,753] [INFO] Found 6/6 markers.
[2024-01-25 19:38:58,779] [INFO] Query marker FASTA was written to GCF_014837015.1_ASM1483701v1_genomic.fna/markers.fasta
[2024-01-25 19:38:58,779] [INFO] Task started: Blastn
[2024-01-25 19:38:58,780] [INFO] Running command: blastn -query GCF_014837015.1_ASM1483701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/reference_markers.fasta -out GCF_014837015.1_ASM1483701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:59,449] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:59,457] [INFO] Selected 11 target genomes.
[2024-01-25 19:38:59,458] [INFO] Target genome list was writen to GCF_014837015.1_ASM1483701v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:59,465] [INFO] Task started: fastANI
[2024-01-25 19:38:59,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg148b37df-1a90-483c-b65d-c2e473775d56/GCF_014837015.1_ASM1483701v1_genomic.fna.gz --refList GCF_014837015.1_ASM1483701v1_genomic.fna/target_genomes.txt --output GCF_014837015.1_ASM1483701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:07,758] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:07,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:07,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:07,768] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:39:07,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:07,768] [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
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	100.0	1045	1048	95	conclusive
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	90.637	883	1048	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	90.5339	900	1048	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	86.9499	818	1048	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	83.701	764	1048	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	83.1464	689	1048	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	80.2835	540	1048	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.6064	330	1048	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.9497	278	1048	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	78.9303	281	1048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:07,771] [INFO] DFAST Taxonomy check result was written to GCF_014837015.1_ASM1483701v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:07,774] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:07,774] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:07,774] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/checkm_data
[2024-01-25 19:39:07,775] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:07,817] [INFO] Task started: CheckM
[2024-01-25 19:39:07,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837015.1_ASM1483701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837015.1_ASM1483701v1_genomic.fna/checkm_input GCF_014837015.1_ASM1483701v1_genomic.fna/checkm_result
[2024-01-25 19:39:32,939] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:32,940] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:32,951] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:32,951] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:32,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837015.1_ASM1483701v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:32,952] [INFO] Task started: Blastn
[2024-01-25 19:39:32,952] [INFO] Running command: blastn -query GCF_014837015.1_ASM1483701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c84875c-f1b3-4fcf-b04e-a6ce2473646b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837015.1_ASM1483701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:34,057] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:34,060] [INFO] Selected 8 target genomes.
[2024-01-25 19:39:34,060] [INFO] Target genome list was writen to GCF_014837015.1_ASM1483701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:34,067] [INFO] Task started: fastANI
[2024-01-25 19:39:34,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg148b37df-1a90-483c-b65d-c2e473775d56/GCF_014837015.1_ASM1483701v1_genomic.fna.gz --refList GCF_014837015.1_ASM1483701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837015.1_ASM1483701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:39,906] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:39,912] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:39,912] [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_001647535.1	s__Acinetobacter sp001647535	98.5368	942	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.56	98.54	0.92	0.90	3	conclusive
GCF_011058205.1	s__Acinetobacter fasciculus	90.5951	826	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCF_000487975.1	s__Acinetobacter lwoffii	90.548	888	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	99.52	96.36	0.98	0.86	9	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	90.538	854	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	-
GCF_014769185.1	s__Acinetobacter lwoffii_D	90.4914	875	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.35	96.24	0.87	0.85	7	-
GCA_000761495.1	s__Acinetobacter idrijaensis	90.4788	848	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCA_002367455.1	s__Acinetobacter sp002367455	90.2503	716	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0792	96.40	96.39	0.89	0.87	3	-
GCF_019038395.1	s__Acinetobacter sp019038395	89.1737	864	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:39,914] [INFO] GTDB search result was written to GCF_014837015.1_ASM1483701v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:39,914] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:39,917] [INFO] DFAST_QC result json was written to GCF_014837015.1_ASM1483701v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:39,917] [INFO] DFAST_QC completed!
[2024-01-25 19:39:39,917] [INFO] Total running time: 0h0m49s