[2024-01-24 13:28:18,565] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:18,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:18,570] [INFO] DQC Reference Directory: /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference
[2024-01-24 13:28:19,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:19,920] [INFO] Task started: Prodigal
[2024-01-24 13:28:19,922] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bb48595-c87c-4f34-8d2a-0d3336b204c0/GCF_008693045.1_ASM869304v1_genomic.fna.gz | prodigal -d GCF_008693045.1_ASM869304v1_genomic.fna/cds.fna -a GCF_008693045.1_ASM869304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:34,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:34,440] [INFO] Task started: HMMsearch
[2024-01-24 13:28:34,440] [INFO] Running command: hmmsearch --tblout GCF_008693045.1_ASM869304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/reference_markers.hmm GCF_008693045.1_ASM869304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:34,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:34,762] [INFO] Found 6/6 markers.
[2024-01-24 13:28:34,807] [INFO] Query marker FASTA was written to GCF_008693045.1_ASM869304v1_genomic.fna/markers.fasta
[2024-01-24 13:28:34,808] [INFO] Task started: Blastn
[2024-01-24 13:28:34,808] [INFO] Running command: blastn -query GCF_008693045.1_ASM869304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/reference_markers.fasta -out GCF_008693045.1_ASM869304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:35,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:35,769] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:35,770] [INFO] Target genome list was writen to GCF_008693045.1_ASM869304v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:35,777] [INFO] Task started: fastANI
[2024-01-24 13:28:35,777] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb48595-c87c-4f34-8d2a-0d3336b204c0/GCF_008693045.1_ASM869304v1_genomic.fna.gz --refList GCF_008693045.1_ASM869304v1_genomic.fna/target_genomes.txt --output GCF_008693045.1_ASM869304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:53,253] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:53,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:53,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:53,272] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:28:53,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:53,272] [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
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	100.0	1628	1628	95	conclusive
Ewingella americana	strain=ATCC 33852	GCA_000735345.1	41202	41202	type	True	99.976	1573	1628	95	conclusive
Ewingella americana	strain=NCTC12157	GCA_900451015.1	41202	41202	type	True	99.9512	1626	1628	95	conclusive
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	81.7488	941	1628	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	81.6395	924	1628	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003602055.1	58169	58169	type	True	81.6042	934	1628	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	81.5545	897	1628	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	81.5518	943	1628	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	81.5308	959	1628	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	81.4833	911	1628	95	below_threshold
Rahnella contaminans	strain=Lac-M11	GCA_011065485.1	2703882	2703882	type	True	81.325	934	1628	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.7089	657	1628	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.4256	679	1628	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	79.3136	644	1628	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	79.0885	596	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,274] [INFO] DFAST Taxonomy check result was written to GCF_008693045.1_ASM869304v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:53,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:53,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:53,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/checkm_data
[2024-01-24 13:28:53,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:53,323] [INFO] Task started: CheckM
[2024-01-24 13:28:53,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008693045.1_ASM869304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008693045.1_ASM869304v1_genomic.fna/checkm_input GCF_008693045.1_ASM869304v1_genomic.fna/checkm_result
[2024-01-24 13:29:38,232] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:38,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:38,279] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:38,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:38,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008693045.1_ASM869304v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:38,280] [INFO] Task started: Blastn
[2024-01-24 13:29:38,280] [INFO] Running command: blastn -query GCF_008693045.1_ASM869304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga61596eb-0060-47a2-9d25-43c290677c95/dqc_reference/reference_markers_gtdb.fasta -out GCF_008693045.1_ASM869304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:39,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:39,746] [INFO] Selected 17 target genomes.
[2024-01-24 13:29:39,746] [INFO] Target genome list was writen to GCF_008693045.1_ASM869304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:39,768] [INFO] Task started: fastANI
[2024-01-24 13:29:39,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb48595-c87c-4f34-8d2a-0d3336b204c0/GCF_008693045.1_ASM869304v1_genomic.fna.gz --refList GCF_008693045.1_ASM869304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008693045.1_ASM869304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:58,492] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:58,512] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:58,512] [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_000735345.1	s__Ewingella americana	99.976	1573	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	98.48	96.44	0.97	0.94	5	conclusive
GCA_003864575.1	s__Ewingella sp003864575	83.2879	836	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438725.1	s__Ewingella americana_A	82.915	1030	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639435.1	s__Ewingella psychrotolerans	81.7943	845	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Ewingella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004330295.1	s__Rahnella victoriana	81.7468	942	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.74	98.62	0.94	0.93	5	-
GCF_001422575.1	s__Rahnella sp001422575	81.648	921	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	98.18	98.11	0.91	0.87	5	-
GCF_002951615.1	s__Rahnella sp002951615	81.5924	896	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610915.1	s__Rahnella variigena	81.5857	920	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	97.86	97.35	0.92	0.89	8	-
GCF_015644585.1	s__Rahnella laticis	81.5778	953	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	96.65	95.20	0.90	0.83	8	-
GCF_019049675.1	s__Rahnella sp019049675	81.5664	896	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003263515.1	s__Rahnella inusitata	81.5493	943	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.32	98.94	0.97	0.94	4	-
GCF_002834385.1	s__Rahnella sp002834385	81.4455	881	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011684115.1	s__Rahnella aceris	81.373	898	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	99.19	98.40	0.95	0.89	21	-
GCF_009208105.1	s__Rouxiella sp009208105	80.0507	673	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017299535.1	s__Serratia marcescens	79.4273	662	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	96.8494	99.42	98.47	0.97	0.85	72	-
GCF_013375155.1	s__Serratia ureilytica	79.3275	680	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.3985	98.73	97.62	0.94	0.88	142	-
GCF_009817885.1	s__Serratia_B rhizosphaerae	79.0834	595	1628	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_B	95.0	97.16	97.09	0.90	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:58,514] [INFO] GTDB search result was written to GCF_008693045.1_ASM869304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:58,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:58,519] [INFO] DFAST_QC result json was written to GCF_008693045.1_ASM869304v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:58,519] [INFO] DFAST_QC completed!
[2024-01-24 13:29:58,519] [INFO] Total running time: 0h1m40s