[2024-01-25 19:31:51,599] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference
[2024-01-25 19:31:52,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,710] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg50af735f-a72a-4109-bdaf-0aa88182269d/GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna.gz | prodigal -d GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/cds.fna -a GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:01,192] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:01,192] [INFO] Task started: HMMsearch
[2024-01-25 19:32:01,192] [INFO] Running command: hmmsearch --tblout GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/reference_markers.hmm GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:01,409] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:01,410] [INFO] Found 6/6 markers.
[2024-01-25 19:32:01,442] [INFO] Query marker FASTA was written to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/markers.fasta
[2024-01-25 19:32:01,442] [INFO] Task started: Blastn
[2024-01-25 19:32:01,442] [INFO] Running command: blastn -query GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/reference_markers.fasta -out GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:02,090] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:02,094] [INFO] Selected 14 target genomes.
[2024-01-25 19:32:02,094] [INFO] Target genome list was writen to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:02,102] [INFO] Task started: fastANI
[2024-01-25 19:32:02,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg50af735f-a72a-4109-bdaf-0aa88182269d/GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna.gz --refList GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/target_genomes.txt --output GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:14,586] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:14,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:14,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:14,596] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:32:14,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:14,596] [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 vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	99.9803	1319	1361	95	conclusive
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	90.1074	1107	1361	95	below_threshold
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	90.0961	1106	1361	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	85.8347	1014	1361	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	85.4894	998	1361	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	85.478	1005	1361	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	85.4697	933	1361	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.4686	772	1361	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.4606	773	1361	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.9346	719	1361	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.7954	686	1361	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.8515	560	1361	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.7384	570	1361	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.5596	560	1361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:14,598] [INFO] DFAST Taxonomy check result was written to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:14,599] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:14,599] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:14,599] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/checkm_data
[2024-01-25 19:32:14,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:14,656] [INFO] Task started: CheckM
[2024-01-25 19:32:14,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/checkm_input GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/checkm_result
[2024-01-25 19:32:43,453] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:43,454] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:43,478] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:43,479] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:43,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/markers.fasta)
[2024-01-25 19:32:43,480] [INFO] Task started: Blastn
[2024-01-25 19:32:43,480] [INFO] Running command: blastn -query GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4960664-7584-43d8-a218-5b087d0f07ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:44,529] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:44,533] [INFO] Selected 12 target genomes.
[2024-01-25 19:32:44,533] [INFO] Target genome list was writen to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:44,539] [INFO] Task started: fastANI
[2024-01-25 19:32:44,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg50af735f-a72a-4109-bdaf-0aa88182269d/GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna.gz --refList GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:55,977] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:55,986] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:55,986] [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_014635885.1	s__Acinetobacter vivianii	99.9803	1319	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	conclusive
GCF_014635545.1	s__Acinetobacter courvalinii	90.0961	1106	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
GCF_009884975.1	s__Acinetobacter dispersus	86.3809	1015	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000805455.1	s__Acinetobacter sp000805455	86.3022	1007	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367945.1	s__Acinetobacter proteolyticus	85.8535	1015	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369525.1	s__Acinetobacter sp000369525	85.8316	1002	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000400715.1	s__Acinetobacter sp000400715	85.7094	1003	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753255.1	s__Acinetobacter sp011753255	85.6719	971	1361	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	85.4883	944	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	85.4831	1005	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	85.4734	933	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000368585.1	s__Acinetobacter venetianus	83.4695	772	1361	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:55,987] [INFO] GTDB search result was written to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:55,989] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:55,992] [INFO] DFAST_QC result json was written to GCF_000369705.1_Acin_sp_NIPH_2168_V1_genomic.fna/dqc_result.json
[2024-01-25 19:32:55,992] [INFO] DFAST_QC completed!
[2024-01-25 19:32:55,992] [INFO] Total running time: 0h1m4s