[2024-01-24 13:28:01,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,753] [INFO] DQC Reference Directory: /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference
[2024-01-24 13:28:03,135] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,136] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,136] [INFO] Running command: gunzip -c /var/lib/cwl/stga3db0454-9500-4a98-8991-510091524365/GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna.gz | prodigal -d GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/cds.fna -a GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:13,277] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:13,277] [INFO] Task started: HMMsearch
[2024-01-24 13:28:13,277] [INFO] Running command: hmmsearch --tblout GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/reference_markers.hmm GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,549] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,588] [INFO] Query marker FASTA was written to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/markers.fasta
[2024-01-24 13:28:13,589] [INFO] Task started: Blastn
[2024-01-24 13:28:13,589] [INFO] Running command: blastn -query GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/reference_markers.fasta -out GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:14,325] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:14,328] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:14,329] [INFO] Target genome list was writen to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:14,336] [INFO] Task started: fastANI
[2024-01-24 13:28:14,336] [INFO] Running command: fastANI --query /var/lib/cwl/stga3db0454-9500-4a98-8991-510091524365/GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna.gz --refList GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/target_genomes.txt --output GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:26,205] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:26,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:26,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:26,218] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:26,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:26,219] [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 gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	100.0	1396	1399	95	conclusive
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	99.9969	1383	1399	95	conclusive
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	91.739	1163	1399	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	88.8545	1033	1399	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	85.502	996	1399	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	85.322	996	1399	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	84.5035	782	1399	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.3594	785	1399	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	83.135	606	1399	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	82.9423	646	1399	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.6916	739	1399	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.4547	709	1399	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.9472	524	1399	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.9314	519	1399	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.901	529	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:26,220] [INFO] DFAST Taxonomy check result was written to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:26,220] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:26,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:26,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/checkm_data
[2024-01-24 13:28:26,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:26,261] [INFO] Task started: CheckM
[2024-01-24 13:28:26,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/checkm_input GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/checkm_result
[2024-01-24 13:29:01,389] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:01,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:01,406] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:01,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:01,407] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/markers.fasta)
[2024-01-24 13:29:01,407] [INFO] Task started: Blastn
[2024-01-24 13:29:01,407] [INFO] Running command: blastn -query GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stga858ff13-d8bb-406b-80b0-80520d7d1e6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:02,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:02,441] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:02,441] [INFO] Target genome list was writen to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:02,456] [INFO] Task started: fastANI
[2024-01-24 13:29:02,456] [INFO] Running command: fastANI --query /var/lib/cwl/stga3db0454-9500-4a98-8991-510091524365/GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna.gz --refList GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:14,464] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,476] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:14,476] [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_000413855.1	s__Acinetobacter gyllenbergii	100.0	1396	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	conclusive
GCF_013072695.1	s__Acinetobacter sp013072695	92.2146	1173	1399	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	91.7517	1162	1399	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	90.1715	1162	1399	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	90.1196	1140	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	88.8545	1033	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_011753255.1	s__Acinetobacter sp011753255	88.5694	1075	1399	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	88.5559	1044	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_009884975.1	s__Acinetobacter dispersus	88.1286	1093	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_014635885.1	s__Acinetobacter vivianii	85.4867	998	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_014636095.1	s__Acinetobacter modestus	84.5134	781	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_002165255.2	s__Acinetobacter sp002165255	84.0692	711	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000368025.1	s__Acinetobacter parvus	82.9619	644	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,478] [INFO] GTDB search result was written to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:14,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:14,483] [INFO] DFAST_QC result json was written to GCF_000413855.1_Acin_gyll_CIP_110306_V1_genomic.fna/dqc_result.json
[2024-01-24 13:29:14,483] [INFO] DFAST_QC completed!
[2024-01-24 13:29:14,483] [INFO] Total running time: 0h1m13s