[2024-01-25 20:03:05,726] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference
[2024-01-25 20:03:06,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,889] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg77fd9d93-af54-4671-924c-86c192aebd90/GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna.gz | prodigal -d GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/cds.fna -a GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:13,985] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:13,985] [INFO] Task started: HMMsearch
[2024-01-25 20:03:13,985] [INFO] Running command: hmmsearch --tblout GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/reference_markers.hmm GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:14,196] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:14,197] [INFO] Found 6/6 markers.
[2024-01-25 20:03:14,230] [INFO] Query marker FASTA was written to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/markers.fasta
[2024-01-25 20:03:14,230] [INFO] Task started: Blastn
[2024-01-25 20:03:14,230] [INFO] Running command: blastn -query GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/reference_markers.fasta -out GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:14,829] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:14,832] [INFO] Selected 16 target genomes.
[2024-01-25 20:03:14,832] [INFO] Target genome list was writen to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:14,848] [INFO] Task started: fastANI
[2024-01-25 20:03:14,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg77fd9d93-af54-4671-924c-86c192aebd90/GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna.gz --refList GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/target_genomes.txt --output GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:27,540] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:27,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:27,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:27,551] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:27,552] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:27,552] [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 variabilis	strain=NIPH 2171	GCA_000369625.1	70346	70346	type	True	99.9981	1157	1163	95	conclusive
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	84.9478	815	1163	95	below_threshold
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	84.8041	826	1163	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	83.9678	719	1163	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	83.6968	764	1163	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	83.6212	760	1163	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	82.1814	600	1163	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	81.6512	577	1163	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	81.5203	506	1163	95	below_threshold
Acinetobacter wanghuae	strain=dk386	GCA_009557235.1	2662362	2662362	type	True	81.098	529	1163	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	80.9423	489	1163	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.7195	477	1163	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.7964	320	1163	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.7768	319	1163	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	79.4226	392	1163	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.2799	378	1163	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:27,553] [INFO] DFAST Taxonomy check result was written to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:27,554] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:27,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:27,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/checkm_data
[2024-01-25 20:03:27,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:27,594] [INFO] Task started: CheckM
[2024-01-25 20:03:27,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/checkm_input GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/checkm_result
[2024-01-25 20:03:54,357] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:54,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:54,387] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:54,388] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:54,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/markers.fasta)
[2024-01-25 20:03:54,388] [INFO] Task started: Blastn
[2024-01-25 20:03:54,388] [INFO] Running command: blastn -query GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8372b68a-42cf-4508-8c1e-048f607a6ff6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:55,235] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:55,242] [INFO] Selected 18 target genomes.
[2024-01-25 20:03:55,243] [INFO] Target genome list was writen to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:55,257] [INFO] Task started: fastANI
[2024-01-25 20:03:55,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg77fd9d93-af54-4671-924c-86c192aebd90/GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna.gz --refList GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:09,711] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:09,723] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:09,723] [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_000369625.1	s__Acinetobacter variabilis	99.9981	1158	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.87	95.07	0.88	0.83	48	conclusive
GCF_011058205.1	s__Acinetobacter fasciculus	84.7632	769	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCF_000487975.1	s__Acinetobacter lwoffii	84.6809	815	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	99.52	96.36	0.98	0.86	9	-
GCA_000761495.1	s__Acinetobacter idrijaensis	84.542	795	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCF_014769185.1	s__Acinetobacter lwoffii_D	84.4885	804	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.35	96.24	0.87	0.85	7	-
GCF_015602705.1	s__Acinetobacter lwoffii_E	84.0368	766	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.0499	96.41	96.41	0.92	0.92	2	-
GCF_002688565.1	s__Acinetobacter sp002688565	84.0033	720	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368625.1	s__Acinetobacter schindleri	83.9621	720	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.30	96.65	0.89	0.83	25	-
GCF_013343215.1	s__Acinetobacter lwoffii_C	83.7166	742	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.90	0.93	0.91	5	-
GCF_001647535.1	s__Acinetobacter sp001647535	83.6515	751	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.56	98.54	0.92	0.90	3	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	83.626	759	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_000773685.1	s__Acinetobacter sp000773685	83.277	639	1163	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	82.3215	555	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000488255.1	s__Acinetobacter indicus	82.2261	600	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCF_016599715.1	s__Acinetobacter sp002135245	81.647	568	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_900096895.1	s__Acinetobacter kookii	80.9536	557	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.51	0.92	0.92	2	-
GCF_003024525.3	s__Acinetobacter cumulans	80.9291	490	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_013009345.1	s__Acinetobacter sp013009345	80.1625	316	1163	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:09,724] [INFO] GTDB search result was written to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:09,725] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:09,728] [INFO] DFAST_QC result json was written to GCF_000369625.1_Acin_sp_NIPH_2171_V1_genomic.fna/dqc_result.json
[2024-01-25 20:04:09,729] [INFO] DFAST_QC completed!
[2024-01-25 20:04:09,729] [INFO] Total running time: 0h1m4s