[2024-01-24 15:18:35,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:35,335] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:35,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference
[2024-01-24 15:18:38,358] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:38,361] [INFO] Task started: Prodigal
[2024-01-24 15:18:38,361] [INFO] Running command: gunzip -c /var/lib/cwl/stga70695fc-3332-411b-a3ae-4ca9c36a2f61/GCF_026344175.1_ASM2634417v1_genomic.fna.gz | prodigal -d GCF_026344175.1_ASM2634417v1_genomic.fna/cds.fna -a GCF_026344175.1_ASM2634417v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:48,800] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:48,801] [INFO] Task started: HMMsearch
[2024-01-24 15:18:48,801] [INFO] Running command: hmmsearch --tblout GCF_026344175.1_ASM2634417v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/reference_markers.hmm GCF_026344175.1_ASM2634417v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:49,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:49,188] [INFO] Found 6/6 markers.
[2024-01-24 15:18:49,240] [INFO] Query marker FASTA was written to GCF_026344175.1_ASM2634417v1_genomic.fna/markers.fasta
[2024-01-24 15:18:49,241] [INFO] Task started: Blastn
[2024-01-24 15:18:49,241] [INFO] Running command: blastn -query GCF_026344175.1_ASM2634417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/reference_markers.fasta -out GCF_026344175.1_ASM2634417v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:49,988] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:49,992] [INFO] Selected 14 target genomes.
[2024-01-24 15:18:49,992] [INFO] Target genome list was writen to GCF_026344175.1_ASM2634417v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:50,001] [INFO] Task started: fastANI
[2024-01-24 15:18:50,002] [INFO] Running command: fastANI --query /var/lib/cwl/stga70695fc-3332-411b-a3ae-4ca9c36a2f61/GCF_026344175.1_ASM2634417v1_genomic.fna.gz --refList GCF_026344175.1_ASM2634417v1_genomic.fna/target_genomes.txt --output GCF_026344175.1_ASM2634417v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:01,981] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:01,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:01,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:01,994] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:01,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:01,995] [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 bereziniae	strain=CIP 70.12	GCA_000368925.1	106648	106648	type	True	90.3132	1227	1437	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	83.3176	1006	1437	95	below_threshold
Acinetobacter guillouiae	strain=CCUG 2491	GCA_008802215.1	106649	106649	type	True	83.299	995	1437	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	81.6481	769	1437	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	81.3093	694	1437	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	81.2787	690	1437	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	80.4253	598	1437	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7588	510	1437	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	79.4407	390	1437	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.4135	408	1437	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	79.0585	374	1437	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	78.8497	346	1437	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.7746	385	1437	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.5415	372	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:01,996] [INFO] DFAST Taxonomy check result was written to GCF_026344175.1_ASM2634417v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:01,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:01,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:01,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/checkm_data
[2024-01-24 15:19:01,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:02,042] [INFO] Task started: CheckM
[2024-01-24 15:19:02,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344175.1_ASM2634417v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344175.1_ASM2634417v1_genomic.fna/checkm_input GCF_026344175.1_ASM2634417v1_genomic.fna/checkm_result
[2024-01-24 15:19:39,564] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:39,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,584] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:39,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:39,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344175.1_ASM2634417v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:39,586] [INFO] Task started: Blastn
[2024-01-24 15:19:39,586] [INFO] Running command: blastn -query GCF_026344175.1_ASM2634417v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2d01bac-acf1-4339-bdfe-fb829a5e94d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344175.1_ASM2634417v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,673] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,678] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:40,678] [INFO] Target genome list was writen to GCF_026344175.1_ASM2634417v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,687] [INFO] Task started: fastANI
[2024-01-24 15:19:40,687] [INFO] Running command: fastANI --query /var/lib/cwl/stga70695fc-3332-411b-a3ae-4ca9c36a2f61/GCF_026344175.1_ASM2634417v1_genomic.fna.gz --refList GCF_026344175.1_ASM2634417v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344175.1_ASM2634417v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:50,763] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:50,777] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:50,777] [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_016508585.1	s__Acinetobacter baumannii_B	96.2543	1195	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.90	99.88	0.97	0.96	14	conclusive
GCF_000368925.1	s__Acinetobacter bereziniae	90.3261	1226	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	87.8602	1056	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	83.3239	1005	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_001696605.3	s__Acinetobacter wuhouensis	81.6387	770	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.82	96.71	0.87	0.86	6	-
GCF_000214135.1	s__Acinetobacter sp000214135	81.3298	708	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611475.1	s__Acinetobacter rongchengensis	81.2993	695	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002233755.1	s__Acinetobacter piscicola	81.2849	689	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902809855.1	s__Acinetobacter sp902809855	80.38	566	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135235.1	s__Acinetobacter sp002135235	79.7685	509	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766635.1	s__Acinetobacter sp900766635	79.1111	177	1437	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:50,778] [INFO] GTDB search result was written to GCF_026344175.1_ASM2634417v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:50,779] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:50,782] [INFO] DFAST_QC result json was written to GCF_026344175.1_ASM2634417v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:50,783] [INFO] DFAST_QC completed!
[2024-01-24 15:19:50,783] [INFO] Total running time: 0h1m15s