[2024-01-24 13:41:10,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference
[2024-01-24 13:41:11,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,613] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,614] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f1efa1f-883e-461d-ae24-cc4f4699517e/GCF_000621045.1_ASM62104v1_genomic.fna.gz | prodigal -d GCF_000621045.1_ASM62104v1_genomic.fna/cds.fna -a GCF_000621045.1_ASM62104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:20,727] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:20,727] [INFO] Task started: HMMsearch
[2024-01-24 13:41:20,727] [INFO] Running command: hmmsearch --tblout GCF_000621045.1_ASM62104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/reference_markers.hmm GCF_000621045.1_ASM62104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:20,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:21,001] [INFO] Found 6/6 markers.
[2024-01-24 13:41:21,037] [INFO] Query marker FASTA was written to GCF_000621045.1_ASM62104v1_genomic.fna/markers.fasta
[2024-01-24 13:41:21,037] [INFO] Task started: Blastn
[2024-01-24 13:41:21,037] [INFO] Running command: blastn -query GCF_000621045.1_ASM62104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/reference_markers.fasta -out GCF_000621045.1_ASM62104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:21,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:21,739] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:21,739] [INFO] Target genome list was writen to GCF_000621045.1_ASM62104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:21,743] [INFO] Task started: fastANI
[2024-01-24 13:41:21,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f1efa1f-883e-461d-ae24-cc4f4699517e/GCF_000621045.1_ASM62104v1_genomic.fna.gz --refList GCF_000621045.1_ASM62104v1_genomic.fna/target_genomes.txt --output GCF_000621045.1_ASM62104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:33,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:33,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:33,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:33,362] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:33,363] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:33,363] [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 baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	100.0	1184	1187	95	conclusive
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	99.9479	1172	1187	95	conclusive
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	82.9858	693	1187	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	80.6018	521	1187	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	80.5221	541	1187	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	80.4243	546	1187	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	80.4151	535	1187	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	80.2757	529	1187	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.4332	406	1187	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.3746	405	1187	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.2184	344	1187	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.9412	332	1187	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.9237	297	1187	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.9033	334	1187	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	78.8756	333	1187	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	78.7959	363	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,365] [INFO] DFAST Taxonomy check result was written to GCF_000621045.1_ASM62104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:33,365] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:33,366] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:33,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/checkm_data
[2024-01-24 13:41:33,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:33,409] [INFO] Task started: CheckM
[2024-01-24 13:41:33,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621045.1_ASM62104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621045.1_ASM62104v1_genomic.fna/checkm_input GCF_000621045.1_ASM62104v1_genomic.fna/checkm_result
[2024-01-24 13:42:06,095] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:06,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,120] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:06,120] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:06,121] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621045.1_ASM62104v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:06,121] [INFO] Task started: Blastn
[2024-01-24 13:42:06,122] [INFO] Running command: blastn -query GCF_000621045.1_ASM62104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57dc251d-d365-4778-84da-e1f85577b58f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621045.1_ASM62104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:07,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:07,005] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:07,005] [INFO] Target genome list was writen to GCF_000621045.1_ASM62104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:07,013] [INFO] Task started: fastANI
[2024-01-24 13:42:07,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f1efa1f-883e-461d-ae24-cc4f4699517e/GCF_000621045.1_ASM62104v1_genomic.fna.gz --refList GCF_000621045.1_ASM62104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621045.1_ASM62104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:15,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:16,011] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:16,011] [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_000368685.1	s__Acinetobacter baylyi	99.9479	1172	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	conclusive
GCF_000760595.1	s__Acinetobacter soli	82.9982	692	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	-
GCF_000368825.1	s__Acinetobacter ursingii	80.6007	522	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
GCF_900625095.1	s__Acinetobacter sp900625095	80.4244	546	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372255.1	s__Acinetobacter guerrae	80.2807	529	1187	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	80.0744	551	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_000369005.1	s__Acinetobacter beijerinckii	79.1688	377	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000368565.1	s__Acinetobacter gerneri	78.989	330	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_000369505.1	s__Acinetobacter sp000369505	78.9616	372	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_900323515.1	s__Acinetobacter stercoris	78.9321	296	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_003024515.2	s__Acinetobacter sichuanensis	78.7959	363	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135375.1	s__Acinetobacter sp002135375	78.7854	235	1187	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	78.59	366	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,013] [INFO] GTDB search result was written to GCF_000621045.1_ASM62104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:16,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:16,017] [INFO] DFAST_QC result json was written to GCF_000621045.1_ASM62104v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:16,017] [INFO] DFAST_QC completed!
[2024-01-24 13:42:16,018] [INFO] Total running time: 0h1m6s