[2024-01-25 19:07:20,540] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference
[2024-01-25 19:07:21,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:21,667] [INFO] Task started: Prodigal
[2024-01-25 19:07:21,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b2ee11f-798f-49d0-8dcd-94646015a36d/GCF_000739855.1_ASM73985v1_genomic.fna.gz | prodigal -d GCF_000739855.1_ASM73985v1_genomic.fna/cds.fna -a GCF_000739855.1_ASM73985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:33,063] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:33,063] [INFO] Task started: HMMsearch
[2024-01-25 19:07:33,063] [INFO] Running command: hmmsearch --tblout GCF_000739855.1_ASM73985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/reference_markers.hmm GCF_000739855.1_ASM73985v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:33,333] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:33,334] [INFO] Found 6/6 markers.
[2024-01-25 19:07:33,369] [INFO] Query marker FASTA was written to GCF_000739855.1_ASM73985v1_genomic.fna/markers.fasta
[2024-01-25 19:07:33,370] [INFO] Task started: Blastn
[2024-01-25 19:07:33,370] [INFO] Running command: blastn -query GCF_000739855.1_ASM73985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/reference_markers.fasta -out GCF_000739855.1_ASM73985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:34,101] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:34,103] [INFO] Selected 11 target genomes.
[2024-01-25 19:07:34,103] [INFO] Target genome list was writen to GCF_000739855.1_ASM73985v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:34,111] [INFO] Task started: fastANI
[2024-01-25 19:07:34,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2ee11f-798f-49d0-8dcd-94646015a36d/GCF_000739855.1_ASM73985v1_genomic.fna.gz --refList GCF_000739855.1_ASM73985v1_genomic.fna/target_genomes.txt --output GCF_000739855.1_ASM73985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:44,000] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:44,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:44,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:44,008] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:07:44,008] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:44,009] [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	100.0	1331	1331	95	conclusive
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	99.9974	1329	1331	95	conclusive
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	99.9954	1330	1331	95	conclusive
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	99.9947	1327	1331	95	conclusive
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	87.3292	1053	1331	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	86.7173	1139	1331	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.2169	123	1331	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.0558	205	1331	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.9569	181	1331	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.3813	79	1331	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	76.3114	65	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:44,010] [INFO] DFAST Taxonomy check result was written to GCF_000739855.1_ASM73985v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:44,010] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:44,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:44,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/checkm_data
[2024-01-25 19:07:44,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:44,053] [INFO] Task started: CheckM
[2024-01-25 19:07:44,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000739855.1_ASM73985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000739855.1_ASM73985v1_genomic.fna/checkm_input GCF_000739855.1_ASM73985v1_genomic.fna/checkm_result
[2024-01-25 19:08:19,148] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:19,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:19,184] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:19,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:19,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000739855.1_ASM73985v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:19,186] [INFO] Task started: Blastn
[2024-01-25 19:08:19,186] [INFO] Running command: blastn -query GCF_000739855.1_ASM73985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dcb24f6-5480-45b6-a720-0393166202f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000739855.1_ASM73985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:20,487] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:20,490] [INFO] Selected 5 target genomes.
[2024-01-25 19:08:20,490] [INFO] Target genome list was writen to GCF_000739855.1_ASM73985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:20,495] [INFO] Task started: fastANI
[2024-01-25 19:08:20,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2ee11f-798f-49d0-8dcd-94646015a36d/GCF_000739855.1_ASM73985v1_genomic.fna.gz --refList GCF_000739855.1_ASM73985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000739855.1_ASM73985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:08:25,860] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:25,865] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:08:25,865] [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	99.9954	1330	1331	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	93.491	1193	1331	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	92.6463	1211	1331	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	90.9171	1128	1331	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	89.6926	1152	1331	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 19:08:25,866] [INFO] GTDB search result was written to GCF_000739855.1_ASM73985v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:08:25,867] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:08:25,875] [INFO] DFAST_QC result json was written to GCF_000739855.1_ASM73985v1_genomic.fna/dqc_result.json
[2024-01-25 19:08:25,875] [INFO] DFAST_QC completed!
[2024-01-25 19:08:25,875] [INFO] Total running time: 0h1m5s