[2024-01-25 18:58:50,875] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:50,877] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:50,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference
[2024-01-25 18:58:52,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:52,081] [INFO] Task started: Prodigal
[2024-01-25 18:58:52,081] [INFO] Running command: gunzip -c /var/lib/cwl/stgeeb51596-1418-4609-a9a0-694c5571410c/GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna.gz | prodigal -d GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/cds.fna -a GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:00,794] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:00,795] [INFO] Task started: HMMsearch
[2024-01-25 18:59:00,795] [INFO] Running command: hmmsearch --tblout GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/reference_markers.hmm GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:01,047] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:01,048] [INFO] Found 6/6 markers.
[2024-01-25 18:59:01,081] [INFO] Query marker FASTA was written to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/markers.fasta
[2024-01-25 18:59:01,081] [INFO] Task started: Blastn
[2024-01-25 18:59:01,081] [INFO] Running command: blastn -query GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/reference_markers.fasta -out GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:01,725] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:01,728] [INFO] Selected 19 target genomes.
[2024-01-25 18:59:01,728] [INFO] Target genome list was writen to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:01,734] [INFO] Task started: fastANI
[2024-01-25 18:59:01,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb51596-1418-4609-a9a0-694c5571410c/GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna.gz --refList GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/target_genomes.txt --output GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:17,689] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:17,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:17,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:17,701] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:59:17,701] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:59:17,701] [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 proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	89.2269	1106	1366	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	88.333	1073	1366	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	88.3073	1080	1366	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	86.849	1005	1366	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	86.2068	1006	1366	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	85.7095	1013	1366	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	84.3313	803	1366	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	83.9559	803	1366	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	83.9486	803	1366	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	83.9316	813	1366	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.5975	786	1366	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.5963	801	1366	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	83.3486	651	1366	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	83.3101	605	1366	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.9668	724	1366	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.8407	717	1366	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.2717	541	1366	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.1907	545	1366	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.2377	423	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:17,702] [INFO] DFAST Taxonomy check result was written to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:17,703] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:17,703] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:17,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/checkm_data
[2024-01-25 18:59:17,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:17,745] [INFO] Task started: CheckM
[2024-01-25 18:59:17,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/checkm_input GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/checkm_result
[2024-01-25 18:59:48,477] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:48,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:48,500] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:48,500] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:48,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/markers.fasta)
[2024-01-25 18:59:48,501] [INFO] Task started: Blastn
[2024-01-25 18:59:48,501] [INFO] Running command: blastn -query GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c153718-fe26-4deb-9223-376a3ee3bbfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:49,568] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:49,571] [INFO] Selected 10 target genomes.
[2024-01-25 18:59:49,571] [INFO] Target genome list was writen to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:49,573] [INFO] Task started: fastANI
[2024-01-25 18:59:49,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgeeb51596-1418-4609-a9a0-694c5571410c/GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna.gz --refList GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:59,608] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:59,615] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:59,615] [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_009884975.1	s__Acinetobacter dispersus	96.8429	1181	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	conclusive
GCF_000369525.1	s__Acinetobacter sp000369525	92.3863	1107	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_011753255.1	s__Acinetobacter sp011753255	91.5306	1098	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400715.1	s__Acinetobacter sp000400715	91.3142	1109	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369405.1	s__Acinetobacter sp000369405	90.349	1112	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072695.1	s__Acinetobacter sp013072695	90.3141	1100	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369805.1	s__Acinetobacter sp000369805	89.6525	1132	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	88.3355	1072	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_014636095.1	s__Acinetobacter modestus	84.302	806	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000369005.1	s__Acinetobacter beijerinckii	83.8064	846	1366	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:59,616] [INFO] GTDB search result was written to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:59,617] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:59,619] [INFO] DFAST_QC result json was written to GCF_000369485.1_Acin_sp_ANC_4105_V1_genomic.fna/dqc_result.json
[2024-01-25 18:59:59,620] [INFO] DFAST_QC completed!
[2024-01-25 18:59:59,620] [INFO] Total running time: 0h1m9s