[2024-01-24 15:01:23,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:01:23,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:01:23,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference
[2024-01-24 15:01:24,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:01:24,682] [INFO] Task started: Prodigal
[2024-01-24 15:01:24,683] [INFO] Running command: gunzip -c /var/lib/cwl/stg145d353b-bf17-4400-88a1-f4af9b6ba4c1/GCF_000264765.2_ASM26476v2_genomic.fna.gz | prodigal -d GCF_000264765.2_ASM26476v2_genomic.fna/cds.fna -a GCF_000264765.2_ASM26476v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:01:36,432] [INFO] Task succeeded: Prodigal
[2024-01-24 15:01:36,433] [INFO] Task started: HMMsearch
[2024-01-24 15:01:36,433] [INFO] Running command: hmmsearch --tblout GCF_000264765.2_ASM26476v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/reference_markers.hmm GCF_000264765.2_ASM26476v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:01:36,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:01:36,770] [INFO] Found 6/6 markers.
[2024-01-24 15:01:36,810] [INFO] Query marker FASTA was written to GCF_000264765.2_ASM26476v2_genomic.fna/markers.fasta
[2024-01-24 15:01:36,810] [INFO] Task started: Blastn
[2024-01-24 15:01:36,810] [INFO] Running command: blastn -query GCF_000264765.2_ASM26476v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/reference_markers.fasta -out GCF_000264765.2_ASM26476v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:01:37,807] [INFO] Task succeeded: Blastn
[2024-01-24 15:01:37,815] [INFO] Selected 11 target genomes.
[2024-01-24 15:01:37,816] [INFO] Target genome list was writen to GCF_000264765.2_ASM26476v2_genomic.fna/target_genomes.txt
[2024-01-24 15:01:37,824] [INFO] Task started: fastANI
[2024-01-24 15:01:37,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg145d353b-bf17-4400-88a1-f4af9b6ba4c1/GCF_000264765.2_ASM26476v2_genomic.fna.gz --refList GCF_000264765.2_ASM26476v2_genomic.fna/target_genomes.txt --output GCF_000264765.2_ASM26476v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:01:49,224] [INFO] Task succeeded: fastANI
[2024-01-24 15:01:49,224] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:01:49,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:01:49,241] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:01:49,241] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:01:49,242] [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
Edwardsiella anguillarum	strain=ET080813	GCA_000264765.2	1821960	1821960	type	True	100.0	1441	1442	95	conclusive
Edwardsiella anguillarum	strain=CCUG 64215	GCA_008801815.1	1821960	1821960	type	True	99.9682	1399	1442	95	conclusive
Edwardsiella piscicida	strain=ACC35.1	GCA_001896205.1	1263550	1263550	reftype	True	94.7552	1161	1442	95	below_threshold
Edwardsiella ictaluri	strain=ATCC 33202	GCA_000264785.1	67780	67780	type	True	92.8954	1039	1442	95	below_threshold
Edwardsiella ictaluri	strain=NCTC12122	GCA_900447225.1	67780	67780	type	True	92.8144	1095	1442	95	below_threshold
Edwardsiella tarda	strain=ATCC 15947	GCA_003113495.2	636	636	type	True	84.4417	951	1442	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.8453	505	1442	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.402	535	1442	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.241	501	1442	95	below_threshold
Erwinia aphidicola	strain=X001	GCA_024169515.1	68334	68334	type	True	78.5257	353	1442	95	below_threshold
Erwinia phyllosphaerae	strain=CMYE1	GCA_019132875.1	2853256	2853256	type	True	77.966	278	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:01:49,243] [INFO] DFAST Taxonomy check result was written to GCF_000264765.2_ASM26476v2_genomic.fna/tc_result.tsv
[2024-01-24 15:01:49,244] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:01:49,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:01:49,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/checkm_data
[2024-01-24 15:01:49,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:01:49,294] [INFO] Task started: CheckM
[2024-01-24 15:01:49,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000264765.2_ASM26476v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000264765.2_ASM26476v2_genomic.fna/checkm_input GCF_000264765.2_ASM26476v2_genomic.fna/checkm_result
[2024-01-24 15:02:27,889] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:27,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:27,911] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:27,911] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:27,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000264765.2_ASM26476v2_genomic.fna/markers.fasta)
[2024-01-24 15:02:27,912] [INFO] Task started: Blastn
[2024-01-24 15:02:27,912] [INFO] Running command: blastn -query GCF_000264765.2_ASM26476v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0291b4aa-534e-4cde-a144-951a0541d247/dqc_reference/reference_markers_gtdb.fasta -out GCF_000264765.2_ASM26476v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:29,042] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:29,045] [INFO] Selected 7 target genomes.
[2024-01-24 15:02:29,045] [INFO] Target genome list was writen to GCF_000264765.2_ASM26476v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:29,058] [INFO] Task started: fastANI
[2024-01-24 15:02:29,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg145d353b-bf17-4400-88a1-f4af9b6ba4c1/GCF_000264765.2_ASM26476v2_genomic.fna.gz --refList GCF_000264765.2_ASM26476v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000264765.2_ASM26476v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:02:36,953] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:36,963] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:02:36,964] [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_000264765.2	s__Edwardsiella anguillarum	100.0	1440	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.66	0.99	0.97	9	conclusive
GCF_001896205.1	s__Edwardsiella piscicida	94.7552	1161	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.37	99.20	0.95	0.93	23	-
GCF_000264785.1	s__Edwardsiella ictaluri	92.8953	1039	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.74	99.41	0.96	0.93	11	-
GCF_000341505.1	s__Edwardsiella tarda	84.3405	927	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.01	97.25	0.94	0.84	19	-
GCF_000474215.1	s__Edwardsiella hoshinae	83.3967	853	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Edwardsiella	95.0	99.86	99.58	0.98	0.94	4	-
GCF_900187015.1	s__Serratia ficaria	79.6024	549	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	99.70	99.56	0.95	0.92	5	-
GCA_019132875.1	s__Erwinia sp019132875	77.9983	276	1442	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:02:36,965] [INFO] GTDB search result was written to GCF_000264765.2_ASM26476v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:02:36,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:02:36,969] [INFO] DFAST_QC result json was written to GCF_000264765.2_ASM26476v2_genomic.fna/dqc_result.json
[2024-01-24 15:02:36,969] [INFO] DFAST_QC completed!
[2024-01-24 15:02:36,969] [INFO] Total running time: 0h1m14s