[2024-01-24 12:15:03,975] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference
[2024-01-24 12:15:05,286] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,287] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,287] [INFO] Running command: gunzip -c /var/lib/cwl/stg521f9c4a-1ceb-4063-b095-3b370a865ab8/GCF_002093665.1_ASM209366v1_genomic.fna.gz | prodigal -d GCF_002093665.1_ASM209366v1_genomic.fna/cds.fna -a GCF_002093665.1_ASM209366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:18,193] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:18,193] [INFO] Task started: HMMsearch
[2024-01-24 12:15:18,193] [INFO] Running command: hmmsearch --tblout GCF_002093665.1_ASM209366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/reference_markers.hmm GCF_002093665.1_ASM209366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:18,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:18,519] [INFO] Found 6/6 markers.
[2024-01-24 12:15:18,579] [INFO] Query marker FASTA was written to GCF_002093665.1_ASM209366v1_genomic.fna/markers.fasta
[2024-01-24 12:15:18,579] [INFO] Task started: Blastn
[2024-01-24 12:15:18,579] [INFO] Running command: blastn -query GCF_002093665.1_ASM209366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/reference_markers.fasta -out GCF_002093665.1_ASM209366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:19,594] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:19,598] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:19,598] [INFO] Target genome list was writen to GCF_002093665.1_ASM209366v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:19,609] [INFO] Task started: fastANI
[2024-01-24 12:15:19,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg521f9c4a-1ceb-4063-b095-3b370a865ab8/GCF_002093665.1_ASM209366v1_genomic.fna.gz --refList GCF_002093665.1_ASM209366v1_genomic.fna/target_genomes.txt --output GCF_002093665.1_ASM209366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:35,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:35,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:35,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:35,038] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:35,039] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:35,039] [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 badensis	strain=DSM 100043	GCA_002093665.1	1646377	1646377	type	True	100.0	1553	1556	95	conclusive
Rouxiella silvae	strain=213	GCA_002093625.1	1646373	1646373	type	True	82.9906	1051	1556	95	below_threshold
Rouxiella chamberiensis	strain=130333	GCA_000951135.1	1513468	1513468	type	True	82.7459	992	1556	95	below_threshold
Rouxiella aceris	strain=SAP-1	GCA_012933545.1	2703884	2703884	type	True	81.4805	832	1556	95	below_threshold
Ewingella americana	strain=CCUG 14506T	GCA_008693045.1	41202	41202	type	True	80.4165	663	1556	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	80.2398	670	1556	95	below_threshold
Rahnella woolbedingensis	strain=DSM 27399	GCA_003602095.1	1510574	1510574	type	True	80.1966	652	1556	95	below_threshold
Rahnella rivi	strain=FC061912-K	GCA_019049655.1	2816249	2816249	type	True	80.174	653	1556	95	below_threshold
Rahnella victoriana	strain=DSM 27397	GCA_004330295.1	1510570	1510570	type	True	80.1029	661	1556	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	80.0424	664	1556	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.0849	501	1556	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.0289	539	1556	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.7439	516	1556	95	below_threshold
Serratia rubidaea	strain=CIP 103234	GCA_001304675.1	61652	61652	type	True	78.6777	462	1556	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:35,042] [INFO] DFAST Taxonomy check result was written to GCF_002093665.1_ASM209366v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:35,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:35,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:35,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/checkm_data
[2024-01-24 12:15:35,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:35,095] [INFO] Task started: CheckM
[2024-01-24 12:15:35,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002093665.1_ASM209366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002093665.1_ASM209366v1_genomic.fna/checkm_input GCF_002093665.1_ASM209366v1_genomic.fna/checkm_result
[2024-01-24 12:16:14,665] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:14,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:14,692] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:14,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:14,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002093665.1_ASM209366v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:14,693] [INFO] Task started: Blastn
[2024-01-24 12:16:14,694] [INFO] Running command: blastn -query GCF_002093665.1_ASM209366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cbe06ab-bd4a-444f-9a02-06f1295cc2b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002093665.1_ASM209366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:16,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:16,175] [INFO] Selected 5 target genomes.
[2024-01-24 12:16:16,176] [INFO] Target genome list was writen to GCF_002093665.1_ASM209366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:16,182] [INFO] Task started: fastANI
[2024-01-24 12:16:16,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg521f9c4a-1ceb-4063-b095-3b370a865ab8/GCF_002093665.1_ASM209366v1_genomic.fna.gz --refList GCF_002093665.1_ASM209366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002093665.1_ASM209366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:22,109] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:22,120] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:22,121] [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_002093665.1	s__Rouxiella badensis	100.0	1553	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	99.63	99.57	0.96	0.91	5	conclusive
GCF_009208105.1	s__Rouxiella sp009208105	83.215	1093	1556	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	83.0051	1049	1556	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	82.883	1035	1556	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	82.7524	991	1556	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rouxiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:22,124] [INFO] GTDB search result was written to GCF_002093665.1_ASM209366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:22,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:22,130] [INFO] DFAST_QC result json was written to GCF_002093665.1_ASM209366v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:22,130] [INFO] DFAST_QC completed!
[2024-01-24 12:16:22,131] [INFO] Total running time: 0h1m18s