[2024-01-24 11:05:03,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference
[2024-01-24 11:05:05,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,813] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,814] [INFO] Running command: gunzip -c /var/lib/cwl/stgb3a1687c-b4b9-46e4-be8d-74da1e314aac/GCF_019355995.1_ASM1935599v1_genomic.fna.gz | prodigal -d GCF_019355995.1_ASM1935599v1_genomic.fna/cds.fna -a GCF_019355995.1_ASM1935599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:12,994] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:12,995] [INFO] Task started: HMMsearch
[2024-01-24 11:05:12,995] [INFO] Running command: hmmsearch --tblout GCF_019355995.1_ASM1935599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/reference_markers.hmm GCF_019355995.1_ASM1935599v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:13,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:13,291] [INFO] Found 6/6 markers.
[2024-01-24 11:05:13,340] [INFO] Query marker FASTA was written to GCF_019355995.1_ASM1935599v1_genomic.fna/markers.fasta
[2024-01-24 11:05:13,341] [INFO] Task started: Blastn
[2024-01-24 11:05:13,341] [INFO] Running command: blastn -query GCF_019355995.1_ASM1935599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/reference_markers.fasta -out GCF_019355995.1_ASM1935599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:14,025] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:14,028] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:14,029] [INFO] Target genome list was writen to GCF_019355995.1_ASM1935599v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:14,034] [INFO] Task started: fastANI
[2024-01-24 11:05:14,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a1687c-b4b9-46e4-be8d-74da1e314aac/GCF_019355995.1_ASM1935599v1_genomic.fna.gz --refList GCF_019355995.1_ASM1935599v1_genomic.fna/target_genomes.txt --output GCF_019355995.1_ASM1935599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:27,064] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:27,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:27,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:27,073] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:05:27,074] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:27,074] [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 haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	100.0	1172	1176	95	conclusive
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	99.9952	1170	1176	95	conclusive
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	99.9568	1153	1176	95	conclusive
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	99.8888	1043	1176	95	conclusive
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	84.0591	689	1176	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	84.0299	688	1176	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	82.8276	724	1176	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	82.8267	694	1176	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	82.8007	700	1176	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	82.6721	751	1176	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	82.2983	699	1176	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.3571	360	1176	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.3449	338	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:27,077] [INFO] DFAST Taxonomy check result was written to GCF_019355995.1_ASM1935599v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:27,077] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:27,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:27,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/checkm_data
[2024-01-24 11:05:27,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:27,114] [INFO] Task started: CheckM
[2024-01-24 11:05:27,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019355995.1_ASM1935599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019355995.1_ASM1935599v1_genomic.fna/checkm_input GCF_019355995.1_ASM1935599v1_genomic.fna/checkm_result
[2024-01-24 11:05:53,382] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:53,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:53,402] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:53,403] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:53,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019355995.1_ASM1935599v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:53,403] [INFO] Task started: Blastn
[2024-01-24 11:05:53,403] [INFO] Running command: blastn -query GCF_019355995.1_ASM1935599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg514cc9eb-dab3-40c1-87cf-412baed8672a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019355995.1_ASM1935599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:54,504] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:54,506] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:54,506] [INFO] Target genome list was writen to GCF_019355995.1_ASM1935599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:54,515] [INFO] Task started: fastANI
[2024-01-24 11:05:54,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgb3a1687c-b4b9-46e4-be8d-74da1e314aac/GCF_019355995.1_ASM1935599v1_genomic.fna.gz --refList GCF_019355995.1_ASM1935599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019355995.1_ASM1935599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:08,938] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:08,948] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:08,948] [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_000369065.1	s__Acinetobacter haemolyticus	99.9556	1152	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	conclusive
GCF_008630915.1	s__Acinetobacter sp008630915	93.6781	952	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	92.5882	922	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368765.1	s__Acinetobacter junii	84.0294	688	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_002165255.2	s__Acinetobacter sp002165255	83.6608	620	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000400715.1	s__Acinetobacter sp000400715	83.0888	735	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368585.1	s__Acinetobacter venetianus	82.976	738	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_009884975.1	s__Acinetobacter dispersus	82.8625	739	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_014636095.1	s__Acinetobacter modestus	82.8356	693	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000367945.1	s__Acinetobacter proteolyticus	82.8081	722	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	82.8062	697	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_014635885.1	s__Acinetobacter vivianii	82.7308	694	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000369645.1	s__Acinetobacter sp000369645	82.7064	692	1176	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	82.682	750	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000369805.1	s__Acinetobacter sp000369805	82.6274	735	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635545.1	s__Acinetobacter courvalinii	82.2428	692	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:08,949] [INFO] GTDB search result was written to GCF_019355995.1_ASM1935599v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:08,950] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:08,952] [INFO] DFAST_QC result json was written to GCF_019355995.1_ASM1935599v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:08,953] [INFO] DFAST_QC completed!
[2024-01-24 11:06:08,953] [INFO] Total running time: 0h1m5s