[2023-06-27 11:50:42,093] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:50:42,097] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:50:42,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference
[2023-06-27 11:50:43,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:50:43,231] [INFO] Task started: Prodigal
[2023-06-27 11:50:43,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c81ca40-3502-4418-84f5-0847f36107c4/GCA_002476455.1_ASM247645v1_genomic.fna.gz | prodigal -d GCA_002476455.1_ASM247645v1_genomic.fna/cds.fna -a GCA_002476455.1_ASM247645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:50:55,824] [INFO] Task succeeded: Prodigal
[2023-06-27 11:50:55,824] [INFO] Task started: HMMsearch
[2023-06-27 11:50:55,824] [INFO] Running command: hmmsearch --tblout GCA_002476455.1_ASM247645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/reference_markers.hmm GCA_002476455.1_ASM247645v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:50:56,074] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:50:56,075] [INFO] Found 6/6 markers.
[2023-06-27 11:50:56,126] [INFO] Query marker FASTA was written to GCA_002476455.1_ASM247645v1_genomic.fna/markers.fasta
[2023-06-27 11:50:56,127] [INFO] Task started: Blastn
[2023-06-27 11:50:56,127] [INFO] Running command: blastn -query GCA_002476455.1_ASM247645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/reference_markers.fasta -out GCA_002476455.1_ASM247645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:50:56,870] [INFO] Task succeeded: Blastn
[2023-06-27 11:50:56,891] [INFO] Selected 11 target genomes.
[2023-06-27 11:50:56,892] [INFO] Target genome list was writen to GCA_002476455.1_ASM247645v1_genomic.fna/target_genomes.txt
[2023-06-27 11:50:56,895] [INFO] Task started: fastANI
[2023-06-27 11:50:56,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c81ca40-3502-4418-84f5-0847f36107c4/GCA_002476455.1_ASM247645v1_genomic.fna.gz --refList GCA_002476455.1_ASM247645v1_genomic.fna/target_genomes.txt --output GCA_002476455.1_ASM247645v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:51:07,439] [INFO] Task succeeded: fastANI
[2023-06-27 11:51:07,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:51:07,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:51:07,447] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:51:07,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:51:07,448] [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 faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	93.2082	1154	1326	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	93.185	1165	1326	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	93.1789	1165	1326	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	93.1469	1167	1326	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	87.1039	1047	1326	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	86.7567	1105	1326	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	76.8616	121	1326	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.8539	171	1326	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.8166	183	1326	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.4872	178	1326	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	75.8958	59	1326	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:51:07,449] [INFO] DFAST Taxonomy check result was written to GCA_002476455.1_ASM247645v1_genomic.fna/tc_result.tsv
[2023-06-27 11:51:07,450] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:51:07,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:51:07,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/checkm_data
[2023-06-27 11:51:07,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:51:07,492] [INFO] Task started: CheckM
[2023-06-27 11:51:07,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002476455.1_ASM247645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002476455.1_ASM247645v1_genomic.fna/checkm_input GCA_002476455.1_ASM247645v1_genomic.fna/checkm_result
[2023-06-27 11:51:45,884] [INFO] Task succeeded: CheckM
[2023-06-27 11:51:45,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:51:45,916] [INFO] ===== Completeness check finished =====
[2023-06-27 11:51:45,916] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:51:45,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002476455.1_ASM247645v1_genomic.fna/markers.fasta)
[2023-06-27 11:51:45,919] [INFO] Task started: Blastn
[2023-06-27 11:51:45,919] [INFO] Running command: blastn -query GCA_002476455.1_ASM247645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71dae119-8e71-4805-bfe7-1d9e1d156cb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_002476455.1_ASM247645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:51:47,165] [INFO] Task succeeded: Blastn
[2023-06-27 11:51:47,169] [INFO] Selected 5 target genomes.
[2023-06-27 11:51:47,169] [INFO] Target genome list was writen to GCA_002476455.1_ASM247645v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:51:47,170] [INFO] Task started: fastANI
[2023-06-27 11:51:47,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c81ca40-3502-4418-84f5-0847f36107c4/GCA_002476455.1_ASM247645v1_genomic.fna.gz --refList GCA_002476455.1_ASM247645v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002476455.1_ASM247645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:51:52,584] [INFO] Task succeeded: fastANI
[2023-06-27 11:51:52,589] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 11:51:52,589] [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_005311025.1	s__Alcaligenes phenolicus	96.1507	1210	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	conclusive
GCF_002443155.1	s__Alcaligenes faecalis	93.185	1165	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_009497775.1	s__Alcaligenes faecalis_D	93.0614	1185	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076515.1	s__Alcaligenes aquatilis	89.9919	1112	1326	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	89.3149	1146	1326	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:51:52,591] [INFO] GTDB search result was written to GCA_002476455.1_ASM247645v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:51:52,591] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:51:52,594] [INFO] DFAST_QC result json was written to GCA_002476455.1_ASM247645v1_genomic.fna/dqc_result.json
[2023-06-27 11:51:52,594] [INFO] DFAST_QC completed!
[2023-06-27 11:51:52,594] [INFO] Total running time: 0h1m11s