[2024-01-25 19:09:20,606] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,611] [INFO] DQC Reference Directory: /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference
[2024-01-25 19:09:21,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,754] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,754] [INFO] Running command: gunzip -c /var/lib/cwl/stg663aa406-f47e-4178-b317-7237b47ac261/GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna.gz | prodigal -d GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/cds.fna -a GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:29,235] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:29,236] [INFO] Task started: HMMsearch
[2024-01-25 19:09:29,236] [INFO] Running command: hmmsearch --tblout GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/reference_markers.hmm GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:29,454] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:29,455] [INFO] Found 6/6 markers.
[2024-01-25 19:09:29,487] [INFO] Query marker FASTA was written to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/markers.fasta
[2024-01-25 19:09:29,487] [INFO] Task started: Blastn
[2024-01-25 19:09:29,487] [INFO] Running command: blastn -query GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/reference_markers.fasta -out GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:30,094] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:30,096] [INFO] Selected 16 target genomes.
[2024-01-25 19:09:30,097] [INFO] Target genome list was writen to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:30,108] [INFO] Task started: fastANI
[2024-01-25 19:09:30,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg663aa406-f47e-4178-b317-7237b47ac261/GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna.gz --refList GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/target_genomes.txt --output GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:41,437] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:41,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:41,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:41,448] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:09:41,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:41,448] [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=CIP 107474	GCA_000368685.1	202950	202950	type	True	99.9935	1194	1198	95	conclusive
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	99.9855	1168	1198	95	conclusive
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	82.779	722	1198	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	80.6577	530	1198	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	80.5576	558	1198	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	80.4763	554	1198	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	80.4127	568	1198	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	80.356	531	1198	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.6316	423	1198	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.5916	426	1198	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.5799	340	1198	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.233	347	1198	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.9979	342	1198	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.9156	301	1198	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.9112	339	1198	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	78.717	355	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:41,450] [INFO] DFAST Taxonomy check result was written to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:41,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:41,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:41,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/checkm_data
[2024-01-25 19:09:41,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:41,491] [INFO] Task started: CheckM
[2024-01-25 19:09:41,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/checkm_input GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/checkm_result
[2024-01-25 19:10:08,933] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:08,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:08,961] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:08,961] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:08,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/markers.fasta)
[2024-01-25 19:10:08,963] [INFO] Task started: Blastn
[2024-01-25 19:10:08,963] [INFO] Running command: blastn -query GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg782db0b8-0a8c-4393-a1bd-cb66608390e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:09,789] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:09,793] [INFO] Selected 13 target genomes.
[2024-01-25 19:10:09,793] [INFO] Target genome list was writen to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:09,802] [INFO] Task started: fastANI
[2024-01-25 19:10:09,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg663aa406-f47e-4178-b317-7237b47ac261/GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna.gz --refList GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:19,308] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:19,316] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:19,317] [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	99.9935	1194	1198	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	82.7831	722	1198	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	80.673	528	1198	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	567	1198	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	80.356	531	1198	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	80.2514	537	1198	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	79.5168	363	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000369505.1	s__Acinetobacter sp000369505	79.2355	371	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_000368565.1	s__Acinetobacter gerneri	79.0892	351	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.97	99.97	1.00	0.99	3	-
GCF_900323515.1	s__Acinetobacter stercoris	78.8988	301	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_000368145.1	s__Acinetobacter guillouiae	78.8765	365	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCF_002135375.1	s__Acinetobacter sp002135375	78.7819	251	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024515.2	s__Acinetobacter sichuanensis	78.7048	356	1198	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:19,318] [INFO] GTDB search result was written to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:19,319] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:19,325] [INFO] DFAST_QC result json was written to GCF_000368685.1_Acin_bayl_CIP_107474_V1_genomic.fna/dqc_result.json
[2024-01-25 19:10:19,325] [INFO] DFAST_QC completed!
[2024-01-25 19:10:19,325] [INFO] Total running time: 0h0m59s