[2024-01-24 13:27:45,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:45,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:45,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference
[2024-01-24 13:27:47,032] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,035] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg28e24e15-4bb7-4f78-bc29-d9e1c0d62226/GCF_014636095.1_ASM1463609v1_genomic.fna.gz | prodigal -d GCF_014636095.1_ASM1463609v1_genomic.fna/cds.fna -a GCF_014636095.1_ASM1463609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:55,416] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:55,417] [INFO] Task started: HMMsearch
[2024-01-24 13:27:55,417] [INFO] Running command: hmmsearch --tblout GCF_014636095.1_ASM1463609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/reference_markers.hmm GCF_014636095.1_ASM1463609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:55,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:55,763] [INFO] Found 6/6 markers.
[2024-01-24 13:27:55,793] [INFO] Query marker FASTA was written to GCF_014636095.1_ASM1463609v1_genomic.fna/markers.fasta
[2024-01-24 13:27:55,794] [INFO] Task started: Blastn
[2024-01-24 13:27:55,794] [INFO] Running command: blastn -query GCF_014636095.1_ASM1463609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/reference_markers.fasta -out GCF_014636095.1_ASM1463609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:56,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:56,518] [INFO] Selected 19 target genomes.
[2024-01-24 13:27:56,519] [INFO] Target genome list was writen to GCF_014636095.1_ASM1463609v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:56,529] [INFO] Task started: fastANI
[2024-01-24 13:27:56,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e24e15-4bb7-4f78-bc29-d9e1c0d62226/GCF_014636095.1_ASM1463609v1_genomic.fna.gz --refList GCF_014636095.1_ASM1463609v1_genomic.fna/target_genomes.txt --output GCF_014636095.1_ASM1463609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:10,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:10,730] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:10,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:10,751] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:10,751] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:10,752] [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 modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	100.0	1168	1169	95	conclusive
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	88.1214	920	1169	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	88.04	926	1169	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	87.9814	934	1169	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	85.6513	650	1169	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	85.6364	625	1169	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	84.5739	823	1169	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	84.4098	807	1169	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	84.4003	802	1169	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	84.0845	782	1169	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	83.9309	746	1169	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	83.9299	748	1169	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.6744	767	1169	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.4506	792	1169	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.433	786	1169	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.8435	690	1169	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.3664	484	1169	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.1783	484	1169	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.0831	487	1169	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:10,754] [INFO] DFAST Taxonomy check result was written to GCF_014636095.1_ASM1463609v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:10,754] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:10,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:10,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/checkm_data
[2024-01-24 13:28:10,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:10,796] [INFO] Task started: CheckM
[2024-01-24 13:28:10,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636095.1_ASM1463609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636095.1_ASM1463609v1_genomic.fna/checkm_input GCF_014636095.1_ASM1463609v1_genomic.fna/checkm_result
[2024-01-24 13:28:41,669] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:41,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,690] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:41,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:41,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636095.1_ASM1463609v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:41,692] [INFO] Task started: Blastn
[2024-01-24 13:28:41,692] [INFO] Running command: blastn -query GCF_014636095.1_ASM1463609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcffbb816-91a1-4da1-b66c-7ce8d0d788a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636095.1_ASM1463609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,778] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,782] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:42,782] [INFO] Target genome list was writen to GCF_014636095.1_ASM1463609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:42,800] [INFO] Task started: fastANI
[2024-01-24 13:28:42,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg28e24e15-4bb7-4f78-bc29-d9e1c0d62226/GCF_014636095.1_ASM1463609v1_genomic.fna.gz --refList GCF_014636095.1_ASM1463609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636095.1_ASM1463609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:54,487] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:54,506] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:54,506] [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_014636095.1	s__Acinetobacter modestus	100.0	1168	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	94.6468	846	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	87.9814	934	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCA_003987695.1	s__Acinetobacter sp003987695	87.732	795	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000368025.1	s__Acinetobacter parvus	85.6646	649	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_000369525.1	s__Acinetobacter sp000369525	84.6239	810	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000367945.1	s__Acinetobacter proteolyticus	84.5478	825	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369405.1	s__Acinetobacter sp000369405	84.4707	795	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072695.1	s__Acinetobacter sp013072695	84.4518	837	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	84.4251	800	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000369005.1	s__Acinetobacter beijerinckii	84.3886	813	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000369805.1	s__Acinetobacter sp000369805	84.3297	812	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369645.1	s__Acinetobacter sp000369645	84.1264	790	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	84.0948	781	1169	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:54,508] [INFO] GTDB search result was written to GCF_014636095.1_ASM1463609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:54,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:54,519] [INFO] DFAST_QC result json was written to GCF_014636095.1_ASM1463609v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:54,520] [INFO] DFAST_QC completed!
[2024-01-24 13:28:54,520] [INFO] Total running time: 0h1m9s