[2024-01-25 19:43:05,504] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:05,505] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:05,505] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference
[2024-01-25 19:43:06,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:06,665] [INFO] Task started: Prodigal
[2024-01-25 19:43:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stge814f57b-928c-462e-9c65-7e4b0a796183/GCF_002443155.1_ASM244315v1_genomic.fna.gz | prodigal -d GCF_002443155.1_ASM244315v1_genomic.fna/cds.fna -a GCF_002443155.1_ASM244315v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:20,276] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:20,276] [INFO] Task started: HMMsearch
[2024-01-25 19:43:20,277] [INFO] Running command: hmmsearch --tblout GCF_002443155.1_ASM244315v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/reference_markers.hmm GCF_002443155.1_ASM244315v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:20,571] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:20,572] [INFO] Found 6/6 markers.
[2024-01-25 19:43:20,608] [INFO] Query marker FASTA was written to GCF_002443155.1_ASM244315v1_genomic.fna/markers.fasta
[2024-01-25 19:43:20,608] [INFO] Task started: Blastn
[2024-01-25 19:43:20,608] [INFO] Running command: blastn -query GCF_002443155.1_ASM244315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/reference_markers.fasta -out GCF_002443155.1_ASM244315v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:21,335] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:21,337] [INFO] Selected 11 target genomes.
[2024-01-25 19:43:21,338] [INFO] Target genome list was writen to GCF_002443155.1_ASM244315v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:21,343] [INFO] Task started: fastANI
[2024-01-25 19:43:21,343] [INFO] Running command: fastANI --query /var/lib/cwl/stge814f57b-928c-462e-9c65-7e4b0a796183/GCF_002443155.1_ASM244315v1_genomic.fna.gz --refList GCF_002443155.1_ASM244315v1_genomic.fna/target_genomes.txt --output GCF_002443155.1_ASM244315v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:31,251] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:31,251] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:31,251] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:31,259] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:43:31,259] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:31,260] [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	strain=DSM 30030	GCA_002443155.1	511	511	type	True	100.0	1357	1358	95	conclusive
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	99.9882	1332	1358	95	conclusive
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	99.9829	1329	1358	95	conclusive
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	99.9801	1334	1358	95	conclusive
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	87.2573	1071	1358	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	86.8432	1121	1358	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	77.7294	66	1358	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.3149	213	1358	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.1845	170	1358	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.1552	136	1358	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.6605	80	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:31,261] [INFO] DFAST Taxonomy check result was written to GCF_002443155.1_ASM244315v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:31,261] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:31,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:31,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/checkm_data
[2024-01-25 19:43:31,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:31,304] [INFO] Task started: CheckM
[2024-01-25 19:43:31,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002443155.1_ASM244315v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002443155.1_ASM244315v1_genomic.fna/checkm_input GCF_002443155.1_ASM244315v1_genomic.fna/checkm_result
[2024-01-25 19:44:13,515] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:13,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:13,533] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:13,533] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:13,534] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002443155.1_ASM244315v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:13,535] [INFO] Task started: Blastn
[2024-01-25 19:44:13,535] [INFO] Running command: blastn -query GCF_002443155.1_ASM244315v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b63948c-1de4-41d8-839b-70c6a279ceb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002443155.1_ASM244315v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:14,834] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:14,836] [INFO] Selected 5 target genomes.
[2024-01-25 19:44:14,837] [INFO] Target genome list was writen to GCF_002443155.1_ASM244315v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:14,843] [INFO] Task started: fastANI
[2024-01-25 19:44:14,843] [INFO] Running command: fastANI --query /var/lib/cwl/stge814f57b-928c-462e-9c65-7e4b0a796183/GCF_002443155.1_ASM244315v1_genomic.fna.gz --refList GCF_002443155.1_ASM244315v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002443155.1_ASM244315v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:20,531] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:20,536] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:20,536] [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_002443155.1	s__Alcaligenes faecalis	100.0	1358	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	conclusive
GCF_009497775.1	s__Alcaligenes faecalis_D	93.4005	1209	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005311025.1	s__Alcaligenes phenolicus	92.631	1215	1358	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	90.9158	1128	1358	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	89.7168	1173	1358	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:20,543] [INFO] GTDB search result was written to GCF_002443155.1_ASM244315v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:20,544] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:20,549] [INFO] DFAST_QC result json was written to GCF_002443155.1_ASM244315v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:20,549] [INFO] DFAST_QC completed!
[2024-01-25 19:44:20,549] [INFO] Total running time: 0h1m15s