[2024-01-24 13:36:32,173] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:32,175] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:32,176] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference
[2024-01-24 13:36:33,491] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:33,492] [INFO] Task started: Prodigal
[2024-01-24 13:36:33,492] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc4c398-b979-49c8-bcb4-71cb3a3c52fd/GCF_000382425.1_ASM38242v1_genomic.fna.gz | prodigal -d GCF_000382425.1_ASM38242v1_genomic.fna/cds.fna -a GCF_000382425.1_ASM38242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:46,954] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:46,955] [INFO] Task started: HMMsearch
[2024-01-24 13:36:46,955] [INFO] Running command: hmmsearch --tblout GCF_000382425.1_ASM38242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/reference_markers.hmm GCF_000382425.1_ASM38242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:47,267] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:47,269] [INFO] Found 6/6 markers.
[2024-01-24 13:36:47,304] [INFO] Query marker FASTA was written to GCF_000382425.1_ASM38242v1_genomic.fna/markers.fasta
[2024-01-24 13:36:47,305] [INFO] Task started: Blastn
[2024-01-24 13:36:47,305] [INFO] Running command: blastn -query GCF_000382425.1_ASM38242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/reference_markers.fasta -out GCF_000382425.1_ASM38242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:47,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:47,929] [INFO] Selected 10 target genomes.
[2024-01-24 13:36:47,930] [INFO] Target genome list was writen to GCF_000382425.1_ASM38242v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:47,939] [INFO] Task started: fastANI
[2024-01-24 13:36:47,939] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc4c398-b979-49c8-bcb4-71cb3a3c52fd/GCF_000382425.1_ASM38242v1_genomic.fna.gz --refList GCF_000382425.1_ASM38242v1_genomic.fna/target_genomes.txt --output GCF_000382425.1_ASM38242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:54,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:54,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:54,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:54,821] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:36:54,821] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:54,821] [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
Empedobacter brevis	strain=ATCC 43319	GCA_000382425.1	247	247	type	True	100.0	1247	1249	95	conclusive
Empedobacter brevis	strain=NBRC 14943	GCA_007990795.1	247	247	type	True	99.9727	1203	1249	95	conclusive
Empedobacter tilapiae	strain=MRS2	GCA_004785645.1	2491114	2491114	type	True	84.9435	864	1249	95	below_threshold
Chishuiella changwenlii	strain=CGMCC 1.12707	GCA_014638465.1	1434701	1434701	type	True	80.9628	564	1249	95	below_threshold
Chishuiella changwenlii	strain=DSM 27989	GCA_900142565.1	1434701	1434701	type	True	80.8159	567	1249	95	below_threshold
Faecalibacter bovis	strain=ZY171143	GCA_017948305.1	2898187	2898187	type	True	79.3948	376	1249	95	below_threshold
Faecalibacter macacae	strain=YIM 102668	GCA_003687725.1	1859289	1859289	type	True	79.3871	390	1249	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	75.9316	66	1249	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.7129	53	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:54,823] [INFO] DFAST Taxonomy check result was written to GCF_000382425.1_ASM38242v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:54,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:54,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:54,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/checkm_data
[2024-01-24 13:36:54,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:54,863] [INFO] Task started: CheckM
[2024-01-24 13:36:54,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000382425.1_ASM38242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000382425.1_ASM38242v1_genomic.fna/checkm_input GCF_000382425.1_ASM38242v1_genomic.fna/checkm_result
[2024-01-24 13:37:38,137] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:38,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:38,163] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:38,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:38,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000382425.1_ASM38242v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:38,164] [INFO] Task started: Blastn
[2024-01-24 13:37:38,164] [INFO] Running command: blastn -query GCF_000382425.1_ASM38242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ac85d0a-e4dc-4555-84db-c19708e97406/dqc_reference/reference_markers_gtdb.fasta -out GCF_000382425.1_ASM38242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:39,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:39,091] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:39,091] [INFO] Target genome list was writen to GCF_000382425.1_ASM38242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:39,102] [INFO] Task started: fastANI
[2024-01-24 13:37:39,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc4c398-b979-49c8-bcb4-71cb3a3c52fd/GCF_000382425.1_ASM38242v1_genomic.fna.gz --refList GCF_000382425.1_ASM38242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000382425.1_ASM38242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:45,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:45,251] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:45,252] [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_000382425.1	s__Empedobacter brevis	100.0	1247	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	98.11	96.51	0.89	0.85	7	conclusive
GCA_002378465.1	s__Empedobacter sp002378465	84.9593	739	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.64	95.90	0.90	0.86	24	-
GCF_004785645.1	s__Empedobacter tilapiae	84.9234	866	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013488205.1	s__Empedobacter falsenii_A	84.6691	843	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	97.19	95.74	0.91	0.86	9	-
GCF_013116755.1	s__Empedobacter stercoris	84.0271	674	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Empedobacter	95.0	99.07	99.07	0.96	0.96	2	-
GCF_900115015.1	s__Algoriella xinjiangensis	81.5677	680	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Algoriella	95.0	98.62	97.69	0.94	0.93	3	-
GCF_900142565.1	s__Chishuiella changwenlii	80.8052	568	1249	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chishuiella	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:45,254] [INFO] GTDB search result was written to GCF_000382425.1_ASM38242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:45,254] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:45,260] [INFO] DFAST_QC result json was written to GCF_000382425.1_ASM38242v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:45,260] [INFO] DFAST_QC completed!
[2024-01-24 13:37:45,260] [INFO] Total running time: 0h1m13s