[2024-01-24 14:05:00,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:00,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:00,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference
[2024-01-24 14:05:01,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:01,936] [INFO] Task started: Prodigal
[2024-01-24 14:05:01,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ff9f93c-6577-4c35-89e7-5a9750deea0c/GCF_012933545.1_ASM1293354v1_genomic.fna.gz | prodigal -d GCF_012933545.1_ASM1293354v1_genomic.fna/cds.fna -a GCF_012933545.1_ASM1293354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:16,120] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:16,120] [INFO] Task started: HMMsearch
[2024-01-24 14:05:16,120] [INFO] Running command: hmmsearch --tblout GCF_012933545.1_ASM1293354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/reference_markers.hmm GCF_012933545.1_ASM1293354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:16,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:16,351] [INFO] Found 6/6 markers.
[2024-01-24 14:05:16,390] [INFO] Query marker FASTA was written to GCF_012933545.1_ASM1293354v1_genomic.fna/markers.fasta
[2024-01-24 14:05:16,390] [INFO] Task started: Blastn
[2024-01-24 14:05:16,390] [INFO] Running command: blastn -query GCF_012933545.1_ASM1293354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/reference_markers.fasta -out GCF_012933545.1_ASM1293354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:17,257] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:17,260] [INFO] Selected 14 target genomes.
[2024-01-24 14:05:17,261] [INFO] Target genome list was writen to GCF_012933545.1_ASM1293354v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:17,289] [INFO] Task started: fastANI
[2024-01-24 14:05:17,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff9f93c-6577-4c35-89e7-5a9750deea0c/GCF_012933545.1_ASM1293354v1_genomic.fna.gz --refList GCF_012933545.1_ASM1293354v1_genomic.fna/target_genomes.txt --output GCF_012933545.1_ASM1293354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:31,841] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:31,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:31,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:31,852] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:31,852] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:31,852] [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 aceris	strain=SAP-1	GCA_012933545.1	2703884	2703884	type	True	100.0	1775	1777	95	conclusive
Rouxiella badensis	strain=DSM 100043	GCA_002093665.1	1646377	1646377	type	True	81.6228	804	1777	95	below_threshold
Rouxiella silvae	strain=213	GCA_002093625.1	1646373	1646373	type	True	81.2566	811	1777	95	below_threshold
Rouxiella chamberiensis	strain=130333	GCA_000951135.1	1513468	1513468	type	True	81.229	768	1777	95	below_threshold
Rahnella variigena	strain=CIP 105588	GCA_003610915.1	574964	574964	type	True	79.9923	685	1777	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	79.9371	685	1777	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	79.8847	702	1777	95	below_threshold
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	79.878	634	1777	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	79.8144	730	1777	95	below_threshold
Rahnella aquatilis	strain=CIP 78.65	GCA_000241955.1	34038	34038	suspected-type	True	79.7513	739	1777	95	below_threshold
Rahnella perminowiae	strain=SL6	GCA_019049755.1	2816244	2816244	type	True	79.7335	635	1777	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.881	446	1777	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8188	464	1777	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.5974	494	1777	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:31,855] [INFO] DFAST Taxonomy check result was written to GCF_012933545.1_ASM1293354v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:31,856] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:31,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:31,856] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/checkm_data
[2024-01-24 14:05:31,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:31,934] [INFO] Task started: CheckM
[2024-01-24 14:05:31,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012933545.1_ASM1293354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012933545.1_ASM1293354v1_genomic.fna/checkm_input GCF_012933545.1_ASM1293354v1_genomic.fna/checkm_result
[2024-01-24 14:06:17,267] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:17,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:17,285] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:17,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:17,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012933545.1_ASM1293354v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:17,286] [INFO] Task started: Blastn
[2024-01-24 14:06:17,286] [INFO] Running command: blastn -query GCF_012933545.1_ASM1293354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4358c45-712d-436f-8709-74244df8026a/dqc_reference/reference_markers_gtdb.fasta -out GCF_012933545.1_ASM1293354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:18,633] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:18,637] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:18,637] [INFO] Target genome list was writen to GCF_012933545.1_ASM1293354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:18,645] [INFO] Task started: fastANI
[2024-01-24 14:06:18,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ff9f93c-6577-4c35-89e7-5a9750deea0c/GCF_012933545.1_ASM1293354v1_genomic.fna.gz --refList GCF_012933545.1_ASM1293354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012933545.1_ASM1293354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:27,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:27,704] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:27,704] [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_012933545.1	s__Rouxiella aceris	100.0	1775	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002093665.1	s__Rouxiella badensis	81.6139	805	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	99.63	99.57	0.96	0.91	5	-
GCF_009208105.1	s__Rouxiella sp009208105	81.4616	848	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093625.1	s__Rouxiella silvae	81.2535	811	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	99.08	98.74	0.93	0.93	3	-
GCF_000257645.1	s__Rouxiella sp000257645	81.2393	797	1777	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	81.2334	767	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019049625.1	s__Rahnella sp019049625	79.8966	701	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590925.1	s__Serratia plymuthica	78.8879	496	1777	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia	95.0	97.90	96.52	0.93	0.88	29	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:27,705] [INFO] GTDB search result was written to GCF_012933545.1_ASM1293354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:27,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:27,709] [INFO] DFAST_QC result json was written to GCF_012933545.1_ASM1293354v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:27,709] [INFO] DFAST_QC completed!
[2024-01-24 14:06:27,709] [INFO] Total running time: 0h1m27s