[2024-01-25 18:41:35,760] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:35,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:35,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference
[2024-01-25 18:41:36,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:36,905] [INFO] Task started: Prodigal
[2024-01-25 18:41:36,905] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6e6b203-5dc9-4e6f-be0b-f328c093fd2f/GCF_024721015.1_ASM2472101v1_genomic.fna.gz | prodigal -d GCF_024721015.1_ASM2472101v1_genomic.fna/cds.fna -a GCF_024721015.1_ASM2472101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:46,734] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:46,734] [INFO] Task started: HMMsearch
[2024-01-25 18:41:46,734] [INFO] Running command: hmmsearch --tblout GCF_024721015.1_ASM2472101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/reference_markers.hmm GCF_024721015.1_ASM2472101v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:46,967] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:46,968] [INFO] Found 6/6 markers.
[2024-01-25 18:41:47,005] [INFO] Query marker FASTA was written to GCF_024721015.1_ASM2472101v1_genomic.fna/markers.fasta
[2024-01-25 18:41:47,005] [INFO] Task started: Blastn
[2024-01-25 18:41:47,005] [INFO] Running command: blastn -query GCF_024721015.1_ASM2472101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/reference_markers.fasta -out GCF_024721015.1_ASM2472101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:47,722] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:47,725] [INFO] Selected 22 target genomes.
[2024-01-25 18:41:47,725] [INFO] Target genome list was writen to GCF_024721015.1_ASM2472101v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:47,747] [INFO] Task started: fastANI
[2024-01-25 18:41:47,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e6b203-5dc9-4e6f-be0b-f328c093fd2f/GCF_024721015.1_ASM2472101v1_genomic.fna.gz --refList GCF_024721015.1_ASM2472101v1_genomic.fna/target_genomes.txt --output GCF_024721015.1_ASM2472101v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:07,336] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:07,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:07,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:07,349] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:07,349] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:07,350] [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
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	100.0	1354	1364	95	conclusive
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.2724	924	1364	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	82.9865	887	1364	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	82.5468	852	1364	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	82.3616	732	1364	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	82.2623	763	1364	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	82.2578	793	1364	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	82.2399	795	1364	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	82.2036	838	1364	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	82.0275	745	1364	95	below_threshold
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	81.9993	753	1364	95	below_threshold
Xenorhabdus budapestensis	strain=DSM 16342	GCA_002632465.1	290110	290110	type	True	81.9738	784	1364	95	below_threshold
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	81.9446	793	1364	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	81.9064	756	1364	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	81.8935	774	1364	95	below_threshold
Xenorhabdus indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	81.7206	774	1364	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.9652	363	1364	95	below_threshold
Rahnella bonaserana	strain=H11b	GCA_019049675.1	2816248	2816248	type	True	77.9939	158	1364	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	77.8326	155	1364	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:07,351] [INFO] DFAST Taxonomy check result was written to GCF_024721015.1_ASM2472101v1_genomic.fna/tc_result.tsv
[2024-01-25 18:42:07,351] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:07,351] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:07,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/checkm_data
[2024-01-25 18:42:07,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:07,398] [INFO] Task started: CheckM
[2024-01-25 18:42:07,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721015.1_ASM2472101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721015.1_ASM2472101v1_genomic.fna/checkm_input GCF_024721015.1_ASM2472101v1_genomic.fna/checkm_result
[2024-01-25 18:42:41,243] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:41,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:41,260] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:41,260] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:41,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721015.1_ASM2472101v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:41,261] [INFO] Task started: Blastn
[2024-01-25 18:42:41,261] [INFO] Running command: blastn -query GCF_024721015.1_ASM2472101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg397ffd63-7b90-400c-8149-091a82942e72/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721015.1_ASM2472101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:42,221] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:42,224] [INFO] Selected 14 target genomes.
[2024-01-25 18:42:42,224] [INFO] Target genome list was writen to GCF_024721015.1_ASM2472101v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:42,238] [INFO] Task started: fastANI
[2024-01-25 18:42:42,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6e6b203-5dc9-4e6f-be0b-f328c093fd2f/GCF_024721015.1_ASM2472101v1_genomic.fna.gz --refList GCF_024721015.1_ASM2472101v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721015.1_ASM2472101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:56,885] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:56,894] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:56,895] [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_000973125.1	s__Xenorhabdus bovienii	98.2103	1215	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	conclusive
GCF_000027225.1	s__Xenorhabdus bovienii_C	94.6548	1065	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_016306625.1	s__Xenorhabdus sp016306625	83.3049	920	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632725.1	s__Xenorhabdus hominickii	83.0028	883	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001037465.1	s__Xenorhabdus khoisanae	82.6177	840	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632615.1	s__Xenorhabdus miraniensis	82.5533	854	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_003610465.1	s__Xenorhabdus ehlersii	82.3086	786	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_002127545.1	s__Xenorhabdus beddingii	82.2393	796	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	82.2275	836	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252955.1	s__Xenorhabdus nematophila	82.115	793	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_002632465.1	s__Xenorhabdus budapestensis	81.9603	786	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
GCF_003386665.1	s__Xenorhabdus cabanillasii	81.9515	792	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	81.9008	756	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014467235.1	s__Xenorhabdus indica	81.7297	771	1364	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:56,896] [INFO] GTDB search result was written to GCF_024721015.1_ASM2472101v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:56,897] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:56,900] [INFO] DFAST_QC result json was written to GCF_024721015.1_ASM2472101v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:56,900] [INFO] DFAST_QC completed!
[2024-01-25 18:42:56,900] [INFO] Total running time: 0h1m21s