[2024-01-24 11:35:34,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,322] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference
[2024-01-24 11:35:35,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,534] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg05d64d9e-69af-463c-91c0-9b3d223fd2c6/GCF_019343455.1_ASM1934345v1_genomic.fna.gz | prodigal -d GCF_019343455.1_ASM1934345v1_genomic.fna/cds.fna -a GCF_019343455.1_ASM1934345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:47,953] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:47,954] [INFO] Task started: HMMsearch
[2024-01-24 11:35:47,954] [INFO] Running command: hmmsearch --tblout GCF_019343455.1_ASM1934345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/reference_markers.hmm GCF_019343455.1_ASM1934345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:48,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:48,244] [INFO] Found 6/6 markers.
[2024-01-24 11:35:48,277] [INFO] Query marker FASTA was written to GCF_019343455.1_ASM1934345v1_genomic.fna/markers.fasta
[2024-01-24 11:35:48,278] [INFO] Task started: Blastn
[2024-01-24 11:35:48,278] [INFO] Running command: blastn -query GCF_019343455.1_ASM1934345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/reference_markers.fasta -out GCF_019343455.1_ASM1934345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:49,036] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:49,039] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:49,039] [INFO] Target genome list was writen to GCF_019343455.1_ASM1934345v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:49,043] [INFO] Task started: fastANI
[2024-01-24 11:35:49,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d64d9e-69af-463c-91c0-9b3d223fd2c6/GCF_019343455.1_ASM1934345v1_genomic.fna.gz --refList GCF_019343455.1_ASM1934345v1_genomic.fna/target_genomes.txt --output GCF_019343455.1_ASM1934345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:57,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:57,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:57,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:57,087] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:57,087] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:57,087] [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
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	100.0	1255	1258	95	conclusive
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	87.2689	1068	1258	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	87.2535	1048	1258	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	87.1796	1070	1258	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	87.1533	1063	1258	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.4237	129	1258	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.2421	160	1258	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.1861	184	1258	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	76.6208	64	1258	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	76.1239	83	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:57,088] [INFO] DFAST Taxonomy check result was written to GCF_019343455.1_ASM1934345v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:57,089] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:57,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:57,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/checkm_data
[2024-01-24 11:35:57,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:57,125] [INFO] Task started: CheckM
[2024-01-24 11:35:57,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019343455.1_ASM1934345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019343455.1_ASM1934345v1_genomic.fna/checkm_input GCF_019343455.1_ASM1934345v1_genomic.fna/checkm_result
[2024-01-24 11:36:37,762] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:37,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:37,788] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:37,788] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:37,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019343455.1_ASM1934345v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:37,789] [INFO] Task started: Blastn
[2024-01-24 11:36:37,789] [INFO] Running command: blastn -query GCF_019343455.1_ASM1934345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e87f66c-2d88-4abf-a3a9-50fead6d2af6/dqc_reference/reference_markers_gtdb.fasta -out GCF_019343455.1_ASM1934345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:39,086] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:39,090] [INFO] Selected 6 target genomes.
[2024-01-24 11:36:39,090] [INFO] Target genome list was writen to GCF_019343455.1_ASM1934345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:39,096] [INFO] Task started: fastANI
[2024-01-24 11:36:39,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg05d64d9e-69af-463c-91c0-9b3d223fd2c6/GCF_019343455.1_ASM1934345v1_genomic.fna.gz --refList GCF_019343455.1_ASM1934345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019343455.1_ASM1934345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:44,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:44,791] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:44,791] [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_004319585.1	s__Alcaligenes faecalis_C	99.5162	1209	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.23	0.95	0.93	4	conclusive
GCF_009497775.1	s__Alcaligenes faecalis_D	87.2663	1069	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002443155.1	s__Alcaligenes faecalis	87.2571	1070	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_005311025.1	s__Alcaligenes phenolicus	87.0306	1080	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	-
GCF_003076515.1	s__Alcaligenes aquatilis	86.3067	1030	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_017377875.1	s__Alcaligenes sp017377875	85.8621	1030	1258	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:44,792] [INFO] GTDB search result was written to GCF_019343455.1_ASM1934345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:44,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:44,797] [INFO] DFAST_QC result json was written to GCF_019343455.1_ASM1934345v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:44,797] [INFO] DFAST_QC completed!
[2024-01-24 11:36:44,797] [INFO] Total running time: 0h1m10s