[2024-01-24 13:01:20,391] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:20,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:20,396] [INFO] DQC Reference Directory: /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference
[2024-01-24 13:01:21,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:21,796] [INFO] Task started: Prodigal
[2024-01-24 13:01:21,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc870d08-4ec9-46cd-ad0f-f4a50bc951b4/GCF_009557235.1_ASM955723v1_genomic.fna.gz | prodigal -d GCF_009557235.1_ASM955723v1_genomic.fna/cds.fna -a GCF_009557235.1_ASM955723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:29,005] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:29,005] [INFO] Task started: HMMsearch
[2024-01-24 13:01:29,005] [INFO] Running command: hmmsearch --tblout GCF_009557235.1_ASM955723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/reference_markers.hmm GCF_009557235.1_ASM955723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:29,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:29,261] [INFO] Found 6/6 markers.
[2024-01-24 13:01:29,289] [INFO] Query marker FASTA was written to GCF_009557235.1_ASM955723v1_genomic.fna/markers.fasta
[2024-01-24 13:01:29,290] [INFO] Task started: Blastn
[2024-01-24 13:01:29,290] [INFO] Running command: blastn -query GCF_009557235.1_ASM955723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/reference_markers.fasta -out GCF_009557235.1_ASM955723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:30,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:30,030] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:30,031] [INFO] Target genome list was writen to GCF_009557235.1_ASM955723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:30,043] [INFO] Task started: fastANI
[2024-01-24 13:01:30,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc870d08-4ec9-46cd-ad0f-f4a50bc951b4/GCF_009557235.1_ASM955723v1_genomic.fna.gz --refList GCF_009557235.1_ASM955723v1_genomic.fna/target_genomes.txt --output GCF_009557235.1_ASM955723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:42,561] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:42,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:42,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:42,577] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:42,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:42,577] [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 wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	100.0	922	922	95	conclusive
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	81.5498	504	922	95	below_threshold
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	81.4292	539	922	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	81.3585	525	922	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	81.2164	556	922	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	81.1646	504	922	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	81.1624	527	922	95	below_threshold
Acinetobacter lanii	strain=185	GCA_011578285.1	2715163	2715163	type	True	81.1461	463	922	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	81.0072	505	922	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	81.0015	501	922	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.8994	455	922	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.8126	466	922	95	below_threshold
Acinetobacter shaoyimingii	strain=323-1	GCA_011578045.1	2715164	2715164	type	True	80.7796	458	922	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.5115	467	922	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.1722	381	922	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.616	301	922	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.3819	315	922	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	78.7629	343	922	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.692	330	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:42,579] [INFO] DFAST Taxonomy check result was written to GCF_009557235.1_ASM955723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:42,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:42,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:42,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/checkm_data
[2024-01-24 13:01:42,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:42,610] [INFO] Task started: CheckM
[2024-01-24 13:01:42,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009557235.1_ASM955723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009557235.1_ASM955723v1_genomic.fna/checkm_input GCF_009557235.1_ASM955723v1_genomic.fna/checkm_result
[2024-01-24 13:02:09,683] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:09,684] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:09,712] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:09,712] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:09,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009557235.1_ASM955723v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:09,713] [INFO] Task started: Blastn
[2024-01-24 13:02:09,713] [INFO] Running command: blastn -query GCF_009557235.1_ASM955723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffa77e39-46e1-4c0a-b5a0-02b35eaa936e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009557235.1_ASM955723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,567] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:10,568] [INFO] Target genome list was writen to GCF_009557235.1_ASM955723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:10,584] [INFO] Task started: fastANI
[2024-01-24 13:02:10,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc870d08-4ec9-46cd-ad0f-f4a50bc951b4/GCF_009557235.1_ASM955723v1_genomic.fna.gz --refList GCF_009557235.1_ASM955723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009557235.1_ASM955723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:22,321] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:22,340] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:22,341] [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_009557235.1	s__Acinetobacter wanghuae	100.0	921	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	conclusive
GCF_001647675.1	s__Acinetobacter sp001647675	83.8393	653	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002688565.1	s__Acinetobacter sp002688565	81.5632	542	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	81.4942	560	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	-
GCF_011058205.1	s__Acinetobacter fasciculus	81.397	529	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	81.3668	524	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_019038395.1	s__Acinetobacter sp019038395	81.2595	517	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.84	99.84	0.94	0.94	2	-
GCA_000761495.1	s__Acinetobacter idrijaensis	81.2205	532	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCF_001678755.1	s__Acinetobacter gandensis	81.1827	502	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_011578285.1	s__Acinetobacter lanii	81.1795	463	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.20	97.20	0.92	0.92	2	-
GCF_001647535.1	s__Acinetobacter sp001647535	80.9208	527	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.56	98.54	0.92	0.90	3	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.864	451	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	80.8126	466	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_011578045.1	s__Acinetobacter shaoyimingii	80.7616	456	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.63	98.63	0.95	0.95	2	-
GCF_002135295.1	s__Acinetobacter sp002135295	80.7587	518	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367455.1	s__Acinetobacter sp002367455	80.7364	451	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0792	96.40	96.39	0.89	0.87	3	-
GCF_001707755.1	s__Acinetobacter celticus	80.5134	468	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296655.1	s__Acinetobacter sp002296655	79.8847	407	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
GCF_000368765.1	s__Acinetobacter junii	79.7068	301	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:22,342] [INFO] GTDB search result was written to GCF_009557235.1_ASM955723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:22,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:22,348] [INFO] DFAST_QC result json was written to GCF_009557235.1_ASM955723v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:22,348] [INFO] DFAST_QC completed!
[2024-01-24 13:02:22,348] [INFO] Total running time: 0h1m2s