[2024-01-25 18:44:05,676] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,680] [INFO] DQC Reference Directory: /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference
[2024-01-25 18:44:06,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,796] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf87945b-bfd1-4fce-b5a6-2725b1b0522a/GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna.gz | prodigal -d GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/cds.fna -a GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:13,780] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:13,781] [INFO] Task started: HMMsearch
[2024-01-25 18:44:13,781] [INFO] Running command: hmmsearch --tblout GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/reference_markers.hmm GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:13,998] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:13,999] [INFO] Found 6/6 markers.
[2024-01-25 18:44:14,024] [INFO] Query marker FASTA was written to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/markers.fasta
[2024-01-25 18:44:14,025] [INFO] Task started: Blastn
[2024-01-25 18:44:14,025] [INFO] Running command: blastn -query GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/reference_markers.fasta -out GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:14,668] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:14,671] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:14,671] [INFO] Target genome list was writen to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/target_genomes.txt
[2024-01-25 18:44:14,681] [INFO] Task started: fastANI
[2024-01-25 18:44:14,681] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf87945b-bfd1-4fce-b5a6-2725b1b0522a/GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna.gz --refList GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/target_genomes.txt --output GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:28,632] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:28,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:28,632] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:28,645] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:28,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:28,645] [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 brisouii	strain=CIP 110357	GCA_000488275.1	396323	396323	type	True	100.0	1039	1044	95	conclusive
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	99.975	1006	1044	95	conclusive
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.6525	334	1044	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	79.6522	358	1044	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	79.6012	359	1044	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.5954	293	1044	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.5901	333	1044	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	79.5473	310	1044	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	79.5044	269	1044	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	79.428	299	1044	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	79.3881	360	1044	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	79.3627	310	1044	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	79.3351	310	1044	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	79.33	298	1044	95	below_threshold
Acinetobacter kanungonis	strain=PS-1	GCA_009939195.1	2699469	2699469	type	True	79.3247	371	1044	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	79.3231	330	1044	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.2485	332	1044	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	79.2243	331	1044	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.1258	314	1044	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	78.9385	330	1044	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	78.9173	338	1044	95	below_threshold
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	78.8198	336	1044	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:28,646] [INFO] DFAST Taxonomy check result was written to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/tc_result.tsv
[2024-01-25 18:44:28,647] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:28,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:28,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/checkm_data
[2024-01-25 18:44:28,648] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:28,680] [INFO] Task started: CheckM
[2024-01-25 18:44:28,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/checkm_input GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/checkm_result
[2024-01-25 18:44:54,371] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:54,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:54,387] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:54,387] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:54,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/markers.fasta)
[2024-01-25 18:44:54,387] [INFO] Task started: Blastn
[2024-01-25 18:44:54,388] [INFO] Running command: blastn -query GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/markers.fasta -db /var/lib/cwl/stgcebd1c9f-78dd-40e3-bc44-0285e25df409/dqc_reference/reference_markers_gtdb.fasta -out GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:55,400] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:55,403] [INFO] Selected 7 target genomes.
[2024-01-25 18:44:55,403] [INFO] Target genome list was writen to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:55,411] [INFO] Task started: fastANI
[2024-01-25 18:44:55,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf87945b-bfd1-4fce-b5a6-2725b1b0522a/GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna.gz --refList GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/target_genomes_gtdb.txt --output GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:00,764] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:00,770] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:00,770] [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_000488275.1	s__Acinetobacter brisouii	100.0	1039	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.72	96.16	0.96	0.91	4	conclusive
GCF_000368265.1	s__Acinetobacter sp000368265	93.8625	902	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.49	0.89	0.85	3	-
GCF_004331075.1	s__Acinetobacter sp004331075	93.4411	874	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.07	96.07	0.89	0.89	2	-
GCF_008993995.1	s__Acinetobacter brisouii_A	85.6358	695	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.99	97.99	0.89	0.89	2	-
GCF_003261585.1	s__Acinetobacter sp003261585	85.6167	778	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016599715.1	s__Acinetobacter sp002135245	79.5977	344	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	79.2615	336	1044	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:00,773] [INFO] GTDB search result was written to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:00,774] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:00,777] [INFO] DFAST_QC result json was written to GCF_000488275.1_Acin_bris_CIP110357_V2_genomic.fna/dqc_result.json
[2024-01-25 18:45:00,777] [INFO] DFAST_QC completed!
[2024-01-25 18:45:00,777] [INFO] Total running time: 0h0m55s