[2024-01-25 19:36:35,701] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,703] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,704] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference
[2024-01-25 19:36:36,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,871] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg453519d0-430e-4bf0-9df0-4322ee3faa1c/GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna.gz | prodigal -d GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/cds.fna -a GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:45,200] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:45,200] [INFO] Task started: HMMsearch
[2024-01-25 19:36:45,201] [INFO] Running command: hmmsearch --tblout GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/reference_markers.hmm GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:45,426] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:45,427] [INFO] Found 6/6 markers.
[2024-01-25 19:36:45,459] [INFO] Query marker FASTA was written to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/markers.fasta
[2024-01-25 19:36:45,459] [INFO] Task started: Blastn
[2024-01-25 19:36:45,459] [INFO] Running command: blastn -query GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/reference_markers.fasta -out GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:46,116] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:46,119] [INFO] Selected 13 target genomes.
[2024-01-25 19:36:46,119] [INFO] Target genome list was writen to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:46,120] [INFO] Task started: fastANI
[2024-01-25 19:36:46,120] [INFO] Running command: fastANI --query /var/lib/cwl/stg453519d0-430e-4bf0-9df0-4322ee3faa1c/GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna.gz --refList GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/target_genomes.txt --output GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:57,114] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:57,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:57,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:57,123] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:57,123] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:57,123] [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 colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	99.9985	1290	1293	95	conclusive
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	88.9932	1042	1293	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	88.9735	1042	1293	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	88.145	1039	1293	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	85.4924	911	1293	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	85.2553	925	1293	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.3492	757	1293	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	83.2562	669	1293	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.7966	697	1293	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.7791	705	1293	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.2092	484	1293	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.1628	490	1293	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.0876	510	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:57,125] [INFO] DFAST Taxonomy check result was written to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:57,126] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:57,126] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:57,126] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/checkm_data
[2024-01-25 19:36:57,127] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:57,165] [INFO] Task started: CheckM
[2024-01-25 19:36:57,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/checkm_input GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/checkm_result
[2024-01-25 19:37:26,095] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:26,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:26,114] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:26,114] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:26,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/markers.fasta)
[2024-01-25 19:37:26,115] [INFO] Task started: Blastn
[2024-01-25 19:37:26,115] [INFO] Running command: blastn -query GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa9316cd-0cf0-423a-8bfa-b3e974e4d3f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:27,153] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:27,156] [INFO] Selected 11 target genomes.
[2024-01-25 19:37:27,156] [INFO] Target genome list was writen to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:27,158] [INFO] Task started: fastANI
[2024-01-25 19:37:27,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg453519d0-430e-4bf0-9df0-4322ee3faa1c/GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna.gz --refList GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:38,141] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:38,149] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:38,149] [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_000413935.1	s__Acinetobacter colistiniresistens	99.9985	1290	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	conclusive
GCF_000369645.1	s__Acinetobacter sp000369645	94.8191	1081	1293	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	88.9755	1042	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_013072695.1	s__Acinetobacter sp013072695	88.5556	1063	1293	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	88.1671	1037	1293	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	87.9415	1082	1293	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	87.9266	1043	1293	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	87.0439	988	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635885.1	s__Acinetobacter vivianii	85.4924	911	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_014635545.1	s__Acinetobacter courvalinii	85.2136	927	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
GCF_002165255.2	s__Acinetobacter sp002165255	84.3872	735	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:38,150] [INFO] GTDB search result was written to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:38,151] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:38,153] [INFO] DFAST_QC result json was written to GCF_000413935.1_Acin_sp_NIPH_2036_V1_genomic.fna/dqc_result.json
[2024-01-25 19:37:38,153] [INFO] DFAST_QC completed!
[2024-01-25 19:37:38,153] [INFO] Total running time: 0h1m2s