[2024-01-24 12:54:05,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,426] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference
[2024-01-24 12:54:07,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,723] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg660463a3-5654-4b0d-99f2-14fad6e3bbda/GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna.gz | prodigal -d GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/cds.fna -a GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:15,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:15,908] [INFO] Task started: HMMsearch
[2024-01-24 12:54:15,908] [INFO] Running command: hmmsearch --tblout GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/reference_markers.hmm GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:16,275] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:16,277] [INFO] Found 6/6 markers.
[2024-01-24 12:54:16,310] [INFO] Query marker FASTA was written to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/markers.fasta
[2024-01-24 12:54:16,311] [INFO] Task started: Blastn
[2024-01-24 12:54:16,311] [INFO] Running command: blastn -query GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/reference_markers.fasta -out GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:17,549] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:17,554] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:17,554] [INFO] Target genome list was writen to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/target_genomes.txt
[2024-01-24 12:54:17,702] [INFO] Task started: fastANI
[2024-01-24 12:54:17,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg660463a3-5654-4b0d-99f2-14fad6e3bbda/GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna.gz --refList GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/target_genomes.txt --output GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:32,649] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:32,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:32,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:32,666] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:54:32,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:32,667] [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 indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	100.0	1061	1063	95	conclusive
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	99.9399	969	1063	95	conclusive
Acinetobacter seohaensis	strain=DSM 16313	GCA_018403785.1	281376	281376	type	True	82.2261	536	1063	95	below_threshold
Acinetobacter towneri	strain=CIP 107472	GCA_000368785.1	202956	202956	type	True	81.9026	598	1063	95	below_threshold
Acinetobacter variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	81.8769	626	1063	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	81.8746	534	1063	95	below_threshold
Acinetobacter towneri	strain=DSM 14962	GCA_000688495.1	202956	202956	type	True	81.777	577	1063	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	81.502	592	1063	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.2597	491	1063	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.9521	570	1063	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	80.5658	462	1063	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.4384	441	1063	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	80.3606	454	1063	95	below_threshold
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	80.2252	485	1063	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	80.1474	465	1063	95	below_threshold
Acinetobacter bouvetii	strain=CIP 107468	GCA_000368865.1	202951	202951	type	True	79.9286	475	1063	95	below_threshold
Acinetobacter bouvetii	strain=DSM 14964	GCA_000373725.1	202951	202951	type	True	79.8398	468	1063	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.6988	312	1063	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	79.6478	341	1063	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.638	307	1063	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.1883	352	1063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,668] [INFO] DFAST Taxonomy check result was written to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/tc_result.tsv
[2024-01-24 12:54:32,669] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:32,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:32,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/checkm_data
[2024-01-24 12:54:32,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:32,703] [INFO] Task started: CheckM
[2024-01-24 12:54:32,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/checkm_input GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/checkm_result
[2024-01-24 12:55:03,592] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:03,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:03,617] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:03,617] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:03,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/markers.fasta)
[2024-01-24 12:55:03,618] [INFO] Task started: Blastn
[2024-01-24 12:55:03,618] [INFO] Running command: blastn -query GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd7124a6-f2cd-4919-b758-073bdf4ffed7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:04,805] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:04,809] [INFO] Selected 20 target genomes.
[2024-01-24 12:55:04,809] [INFO] Target genome list was writen to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:04,828] [INFO] Task started: fastANI
[2024-01-24 12:55:04,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg660463a3-5654-4b0d-99f2-14fad6e3bbda/GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna.gz --refList GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:18,872] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:18,891] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:18,892] [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_000488255.1	s__Acinetobacter indicus	100.0	1061	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	conclusive
GCF_001758345.1	s__Acinetobacter towneri_A	82.1901	547	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.24	97.24	0.85	0.85	2	-
GCF_013343215.1	s__Acinetobacter lwoffii_C	81.9393	583	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.90	0.93	0.91	5	-
GCF_012371325.1	s__Acinetobacter sp012371325	81.9049	553	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_000369625.1	s__Acinetobacter variabilis	81.903	629	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	-
GCF_000368625.1	s__Acinetobacter schindleri	81.8848	536	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.30	96.65	0.89	0.83	25	-
GCF_000368785.1	s__Acinetobacter towneri	81.8763	600	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.88	97.09	0.88	0.84	48	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	81.7486	595	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	-
GCA_000761495.1	s__Acinetobacter idrijaensis	81.538	598	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCF_000773685.1	s__Acinetobacter sp000773685	81.4731	539	1063	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	81.2469	531	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647675.1	s__Acinetobacter sp001647675	81.1935	432	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	81.1159	567	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900096895.1	s__Acinetobacter kookii	80.9811	593	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.51	0.92	0.92	2	-
GCF_019038395.1	s__Acinetobacter sp019038395	80.766	552	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.84	99.84	0.94	0.94	2	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.6368	542	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
GCF_000400735.1	s__Acinetobacter tandoii	80.5508	463	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.2444	483	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.2432	453	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_003611465.1	s__Acinetobacter tianfuensis	80.1602	465	1063	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:18,894] [INFO] GTDB search result was written to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:18,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:18,898] [INFO] DFAST_QC result json was written to GCF_000488255.1_Acin_indi_CIP110367_V2_genomic.fna/dqc_result.json
[2024-01-24 12:55:18,899] [INFO] DFAST_QC completed!
[2024-01-24 12:55:18,899] [INFO] Total running time: 0h1m13s