[2024-01-24 13:01:12,336] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference
[2024-01-24 13:01:13,699] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,700] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,701] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb9250a5-1f11-4729-a337-d2c240fa8179/GCF_001982605.1_ASM198260v1_genomic.fna.gz | prodigal -d GCF_001982605.1_ASM198260v1_genomic.fna/cds.fna -a GCF_001982605.1_ASM198260v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:22,120] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:22,121] [INFO] Task started: HMMsearch
[2024-01-24 13:01:22,121] [INFO] Running command: hmmsearch --tblout GCF_001982605.1_ASM198260v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/reference_markers.hmm GCF_001982605.1_ASM198260v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:22,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:22,420] [INFO] Found 6/6 markers.
[2024-01-24 13:01:22,449] [INFO] Query marker FASTA was written to GCF_001982605.1_ASM198260v1_genomic.fna/markers.fasta
[2024-01-24 13:01:22,449] [INFO] Task started: Blastn
[2024-01-24 13:01:22,449] [INFO] Running command: blastn -query GCF_001982605.1_ASM198260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/reference_markers.fasta -out GCF_001982605.1_ASM198260v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:23,131] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:23,135] [INFO] Selected 21 target genomes.
[2024-01-24 13:01:23,135] [INFO] Target genome list was writen to GCF_001982605.1_ASM198260v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:23,140] [INFO] Task started: fastANI
[2024-01-24 13:01:23,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9250a5-1f11-4729-a337-d2c240fa8179/GCF_001982605.1_ASM198260v1_genomic.fna.gz --refList GCF_001982605.1_ASM198260v1_genomic.fna/target_genomes.txt --output GCF_001982605.1_ASM198260v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:35,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:35,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:35,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:35,518] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:01:35,518] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:35,518] [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
Alkanindiges hydrocarboniclasticus	strain=H1	GCA_001982605.1	1907941	1907941	type	True	100.0	1051	1056	95	conclusive
Alkanindiges illinoisensis	strain=DSM 15370	GCA_000619845.1	197183	197183	type	True	86.5217	839	1056	95	below_threshold
Acinetobacter radioresistens	strain=NBRC 102413	GCA_006757745.1	40216	40216	type	True	78.6091	108	1056	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	78.5543	159	1056	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	78.4604	87	1056	95	below_threshold
Acinetobacter schindleri	strain=CIP 107287	GCA_000368625.1	108981	108981	type	True	78.46	104	1056	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	78.3252	86	1056	95	below_threshold
Acinetobacter radioresistens	strain=CIP 103788	GCA_000368905.1	40216	40216	type	True	78.2988	104	1056	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	78.2918	115	1056	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	78.1289	108	1056	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	78.0859	156	1056	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	77.5796	81	1056	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	77.5768	70	1056	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	77.5011	115	1056	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	76.939	119	1056	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	76.8449	75	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:35,520] [INFO] DFAST Taxonomy check result was written to GCF_001982605.1_ASM198260v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:35,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:35,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:35,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/checkm_data
[2024-01-24 13:01:35,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:35,557] [INFO] Task started: CheckM
[2024-01-24 13:01:35,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001982605.1_ASM198260v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001982605.1_ASM198260v1_genomic.fna/checkm_input GCF_001982605.1_ASM198260v1_genomic.fna/checkm_result
[2024-01-24 13:02:06,777] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:06,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:06,797] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:06,798] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:06,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001982605.1_ASM198260v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:06,799] [INFO] Task started: Blastn
[2024-01-24 13:02:06,799] [INFO] Running command: blastn -query GCF_001982605.1_ASM198260v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce1aca1b-14f8-4978-8888-dd9fb9a2b415/dqc_reference/reference_markers_gtdb.fasta -out GCF_001982605.1_ASM198260v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:07,850] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:07,854] [INFO] Selected 12 target genomes.
[2024-01-24 13:02:07,854] [INFO] Target genome list was writen to GCF_001982605.1_ASM198260v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:07,861] [INFO] Task started: fastANI
[2024-01-24 13:02:07,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb9250a5-1f11-4729-a337-d2c240fa8179/GCF_001982605.1_ASM198260v1_genomic.fna.gz --refList GCF_001982605.1_ASM198260v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001982605.1_ASM198260v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:15,174] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:15,185] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:15,185] [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_001982605.1	s__Alkanindiges hydrocarboniclasticus	100.0	1051	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000619845.1	s__Alkanindiges illinoisensis	86.51	840	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004377485.1	s__Alkanindiges illinoisensis_A	85.9592	791	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173455.1	s__Alkanindiges sp004173455	84.309	722	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Alkanindiges	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006757745.1	s__Acinetobacter radioresistens	78.6658	110	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.57	97.95	0.93	0.87	74	-
GCF_000368045.1	s__Acinetobacter johnsonii	78.6033	81	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_000488255.1	s__Acinetobacter indicus	78.5428	160	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.50	96.50	0.90	0.82	131	-
GCA_000761495.1	s__Acinetobacter idrijaensis	78.4507	121	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.62	96.35	0.87	0.83	6	-
GCF_000368025.1	s__Acinetobacter parvus	78.2935	116	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_001696615.3	s__Acinetobacter sp001696615	77.7721	123	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900625095.1	s__Acinetobacter sp900625095	76.939	119	1056	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135435.1	s__Acinetobacter sp002135435	76.5578	96	1056	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 13:02:15,187] [INFO] GTDB search result was written to GCF_001982605.1_ASM198260v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:15,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:15,193] [INFO] DFAST_QC result json was written to GCF_001982605.1_ASM198260v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:15,193] [INFO] DFAST_QC completed!
[2024-01-24 13:02:15,193] [INFO] Total running time: 0h1m3s