[2024-01-25 20:24:05,474] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,475] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference
[2024-01-25 20:24:06,623] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,624] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,625] [INFO] Running command: gunzip -c /var/lib/cwl/stg15a4f845-6bfd-4dea-884c-e9ebfa9f76f5/GCF_002093625.1_ASM209362v1_genomic.fna.gz | prodigal -d GCF_002093625.1_ASM209362v1_genomic.fna/cds.fna -a GCF_002093625.1_ASM209362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:18,196] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:18,196] [INFO] Task started: HMMsearch
[2024-01-25 20:24:18,196] [INFO] Running command: hmmsearch --tblout GCF_002093625.1_ASM209362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/reference_markers.hmm GCF_002093625.1_ASM209362v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:18,506] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:18,506] [INFO] Found 6/6 markers.
[2024-01-25 20:24:18,557] [INFO] Query marker FASTA was written to GCF_002093625.1_ASM209362v1_genomic.fna/markers.fasta
[2024-01-25 20:24:18,558] [INFO] Task started: Blastn
[2024-01-25 20:24:18,558] [INFO] Running command: blastn -query GCF_002093625.1_ASM209362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/reference_markers.fasta -out GCF_002093625.1_ASM209362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:19,398] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:19,401] [INFO] Selected 21 target genomes.
[2024-01-25 20:24:19,401] [INFO] Target genome list was writen to GCF_002093625.1_ASM209362v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:19,432] [INFO] Task started: fastANI
[2024-01-25 20:24:19,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a4f845-6bfd-4dea-884c-e9ebfa9f76f5/GCF_002093625.1_ASM209362v1_genomic.fna.gz --refList GCF_002093625.1_ASM209362v1_genomic.fna/target_genomes.txt --output GCF_002093625.1_ASM209362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:39,668] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:39,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:39,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:39,677] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:24:39,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:39,677] [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
Rouxiella silvae	strain=213	GCA_002093625.1	1646373	1646373	type	True	100.0	1692	1700	95	conclusive
Rouxiella badensis	strain=DSM 100043	GCA_002093665.1	1646377	1646377	type	True	83.0103	1047	1700	95	below_threshold
Rouxiella chamberiensis	strain=130333	GCA_000951135.1	1513468	1513468	type	True	82.449	898	1700	95	below_threshold
Rouxiella aceris	strain=SAP-1	GCA_012933545.1	2703884	2703884	type	True	81.4035	818	1700	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	80.0874	622	1700	95	below_threshold
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	79.9736	656	1700	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	79.8698	662	1700	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	79.8693	636	1700	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	79.8576	639	1700	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.8559	648	1700	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	79.6502	578	1700	95	below_threshold
Serratia rhizosphaerae	strain=KUDC3025	GCA_009817885.1	2597702	2597702	type	True	78.8056	425	1700	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5831	437	1700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:39,679] [INFO] DFAST Taxonomy check result was written to GCF_002093625.1_ASM209362v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:39,679] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:39,679] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:39,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/checkm_data
[2024-01-25 20:24:39,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:39,730] [INFO] Task started: CheckM
[2024-01-25 20:24:39,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002093625.1_ASM209362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002093625.1_ASM209362v1_genomic.fna/checkm_input GCF_002093625.1_ASM209362v1_genomic.fna/checkm_result
[2024-01-25 20:25:15,920] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:15,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:15,937] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:15,937] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:15,938] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002093625.1_ASM209362v1_genomic.fna/markers.fasta)
[2024-01-25 20:25:15,938] [INFO] Task started: Blastn
[2024-01-25 20:25:15,938] [INFO] Running command: blastn -query GCF_002093625.1_ASM209362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd90d5a3-310a-4fd2-bf7c-cfe0d1f8fbf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002093625.1_ASM209362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:17,044] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:17,046] [INFO] Selected 14 target genomes.
[2024-01-25 20:25:17,047] [INFO] Target genome list was writen to GCF_002093625.1_ASM209362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:17,088] [INFO] Task started: fastANI
[2024-01-25 20:25:17,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg15a4f845-6bfd-4dea-884c-e9ebfa9f76f5/GCF_002093625.1_ASM209362v1_genomic.fna.gz --refList GCF_002093625.1_ASM209362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002093625.1_ASM209362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:30,992] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:30,998] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:30,998] [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_002093625.1	s__Rouxiella silvae	100.0	1692	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	99.08	98.74	0.93	0.93	3	conclusive
GCF_009208105.1	s__Rouxiella sp009208105	94.056	1512	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093665.1	s__Rouxiella badensis	83.0215	1046	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	99.63	99.57	0.96	0.91	5	-
GCF_000257645.1	s__Rouxiella sp000257645	82.6612	1016	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000951135.1	s__Rouxiella chamberiensis	82.4508	898	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933545.1	s__Rouxiella aceris	81.413	816	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517405.1	s__Sodalis_A pierantonius	77.3487	180	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_A	96.0224	N/A	N/A	N/A	N/A	1	-
GCF_000517425.1	s__Sodalis_A praecaptivus	77.3355	216	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Sodalis_A	96.0224	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:30,999] [INFO] GTDB search result was written to GCF_002093625.1_ASM209362v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:31,000] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:31,002] [INFO] DFAST_QC result json was written to GCF_002093625.1_ASM209362v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:31,003] [INFO] DFAST_QC completed!
[2024-01-25 20:25:31,003] [INFO] Total running time: 0h1m26s