[2024-01-24 12:23:35,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference
[2024-01-24 12:23:37,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:37,198] [INFO] Task started: Prodigal
[2024-01-24 12:23:37,199] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb1cbff6-9276-418d-8ecf-5e610ef2179c/GCF_019355975.1_ASM1935597v1_genomic.fna.gz | prodigal -d GCF_019355975.1_ASM1935597v1_genomic.fna/cds.fna -a GCF_019355975.1_ASM1935597v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:46,707] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:46,708] [INFO] Task started: HMMsearch
[2024-01-24 12:23:46,708] [INFO] Running command: hmmsearch --tblout GCF_019355975.1_ASM1935597v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/reference_markers.hmm GCF_019355975.1_ASM1935597v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:47,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:47,031] [INFO] Found 6/6 markers.
[2024-01-24 12:23:47,072] [INFO] Query marker FASTA was written to GCF_019355975.1_ASM1935597v1_genomic.fna/markers.fasta
[2024-01-24 12:23:47,072] [INFO] Task started: Blastn
[2024-01-24 12:23:47,072] [INFO] Running command: blastn -query GCF_019355975.1_ASM1935597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/reference_markers.fasta -out GCF_019355975.1_ASM1935597v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:47,726] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:47,732] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:47,733] [INFO] Target genome list was writen to GCF_019355975.1_ASM1935597v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:47,737] [INFO] Task started: fastANI
[2024-01-24 12:23:47,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1cbff6-9276-418d-8ecf-5e610ef2179c/GCF_019355975.1_ASM1935597v1_genomic.fna.gz --refList GCF_019355975.1_ASM1935597v1_genomic.fna/target_genomes.txt --output GCF_019355975.1_ASM1935597v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:55,240] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:55,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:55,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:55,251] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:23:55,252] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:23:55,252] [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 septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	100.0	1279	1286	95	inconclusive
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	97.4899	1014	1286	95	inconclusive
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	97.4327	1044	1286	95	inconclusive
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	88.4191	908	1286	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	84.54	815	1286	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.0046	411	1286	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	80.5821	437	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:55,253] [INFO] DFAST Taxonomy check result was written to GCF_019355975.1_ASM1935597v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:55,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:55,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:55,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/checkm_data
[2024-01-24 12:23:55,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:55,293] [INFO] Task started: CheckM
[2024-01-24 12:23:55,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019355975.1_ASM1935597v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019355975.1_ASM1935597v1_genomic.fna/checkm_input GCF_019355975.1_ASM1935597v1_genomic.fna/checkm_result
[2024-01-24 12:24:28,204] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:28,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:28,235] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:28,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:28,236] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019355975.1_ASM1935597v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:28,236] [INFO] Task started: Blastn
[2024-01-24 12:24:28,236] [INFO] Running command: blastn -query GCF_019355975.1_ASM1935597v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f4a36ee-e02d-47d1-9c30-012610f1f1a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_019355975.1_ASM1935597v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:29,076] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:29,080] [INFO] Selected 10 target genomes.
[2024-01-24 12:24:29,081] [INFO] Target genome list was writen to GCF_019355975.1_ASM1935597v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:29,089] [INFO] Task started: fastANI
[2024-01-24 12:24:29,089] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1cbff6-9276-418d-8ecf-5e610ef2179c/GCF_019355975.1_ASM1935597v1_genomic.fna.gz --refList GCF_019355975.1_ASM1935597v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019355975.1_ASM1935597v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:36,524] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:36,539] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:36,540] [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_000368825.1	s__Acinetobacter ursingii	97.5083	1013	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	conclusive
GCF_009372255.1	s__Acinetobacter guerrae	88.4346	907	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	-
GCF_016624945.1	s__Acinetobacter sp016624945	85.1028	850	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_900625095.1	s__Acinetobacter sp900625095	84.5388	815	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368685.1	s__Acinetobacter baylyi	80.6289	546	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
GCF_000760595.1	s__Acinetobacter soli	79.7312	467	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	-
GCF_000369045.1	s__Acinetobacter pittii	79.5137	438	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_009939195.1	s__Acinetobacter kanungonis	79.3286	402	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_013004375.1	s__Acinetobacter terrae	79.0189	396	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_004331075.1	s__Acinetobacter sp004331075	78.6059	340	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.07	96.07	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:36,542] [INFO] GTDB search result was written to GCF_019355975.1_ASM1935597v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:36,543] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:36,546] [INFO] DFAST_QC result json was written to GCF_019355975.1_ASM1935597v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:36,546] [INFO] DFAST_QC completed!
[2024-01-24 12:24:36,546] [INFO] Total running time: 0h1m1s