[2024-01-24 14:19:45,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference
[2024-01-24 14:19:47,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,131] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,132] [INFO] Running command: gunzip -c /var/lib/cwl/stg41dff760-eff4-4e0e-b46d-70a10c32b47a/GCF_002632465.1_ASM263246v1_genomic.fna.gz | prodigal -d GCF_002632465.1_ASM263246v1_genomic.fna/cds.fna -a GCF_002632465.1_ASM263246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:57,857] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:57,857] [INFO] Task started: HMMsearch
[2024-01-24 14:19:57,857] [INFO] Running command: hmmsearch --tblout GCF_002632465.1_ASM263246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/reference_markers.hmm GCF_002632465.1_ASM263246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:58,163] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:58,165] [INFO] Found 6/6 markers.
[2024-01-24 14:19:58,212] [INFO] Query marker FASTA was written to GCF_002632465.1_ASM263246v1_genomic.fna/markers.fasta
[2024-01-24 14:19:58,212] [INFO] Task started: Blastn
[2024-01-24 14:19:58,212] [INFO] Running command: blastn -query GCF_002632465.1_ASM263246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/reference_markers.fasta -out GCF_002632465.1_ASM263246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:58,939] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:58,941] [INFO] Selected 15 target genomes.
[2024-01-24 14:19:58,941] [INFO] Target genome list was writen to GCF_002632465.1_ASM263246v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:58,969] [INFO] Task started: fastANI
[2024-01-24 14:19:58,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg41dff760-eff4-4e0e-b46d-70a10c32b47a/GCF_002632465.1_ASM263246v1_genomic.fna.gz --refList GCF_002632465.1_ASM263246v1_genomic.fna/target_genomes.txt --output GCF_002632465.1_ASM263246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:16,230] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:16,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:16,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:16,240] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:16,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:16,240] [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 budapestensis	strain=DSM 16342	GCA_002632465.1	290110	290110	type	True	100.0	1365	1369	95	conclusive
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	93.3018	1132	1369	95	below_threshold
Xenorhabdus indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	92.9729	1129	1369	95	below_threshold
Xenorhabdus stockiae	strain=DSM 17904	GCA_002632825.1	351614	351614	type	True	83.9201	946	1369	95	below_threshold
Xenorhabdus innexi	strain=DSM 16336	GCA_002632485.1	290109	290109	type	True	83.5553	937	1369	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.0908	761	1369	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	81.9345	790	1369	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	81.5617	792	1369	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	79.2493	380	1369	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	79.1907	360	1369	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	79.052	357	1369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:16,242] [INFO] DFAST Taxonomy check result was written to GCF_002632465.1_ASM263246v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:16,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:16,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:16,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/checkm_data
[2024-01-24 14:20:16,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:16,294] [INFO] Task started: CheckM
[2024-01-24 14:20:16,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632465.1_ASM263246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632465.1_ASM263246v1_genomic.fna/checkm_input GCF_002632465.1_ASM263246v1_genomic.fna/checkm_result
[2024-01-24 14:20:51,454] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:51,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:51,469] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:51,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:51,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632465.1_ASM263246v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:51,470] [INFO] Task started: Blastn
[2024-01-24 14:20:51,470] [INFO] Running command: blastn -query GCF_002632465.1_ASM263246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b2a99ed-b2be-4b10-9635-4345c23560bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632465.1_ASM263246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:52,428] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:52,431] [INFO] Selected 11 target genomes.
[2024-01-24 14:20:52,431] [INFO] Target genome list was writen to GCF_002632465.1_ASM263246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:52,438] [INFO] Task started: fastANI
[2024-01-24 14:20:52,439] [INFO] Running command: fastANI --query /var/lib/cwl/stg41dff760-eff4-4e0e-b46d-70a10c32b47a/GCF_002632465.1_ASM263246v1_genomic.fna.gz --refList GCF_002632465.1_ASM263246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632465.1_ASM263246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:04,278] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:04,286] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:04,286] [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_002632465.1	s__Xenorhabdus budapestensis	100.0	1364	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	conclusive
GCF_003386665.1	s__Xenorhabdus cabanillasii	93.3089	1132	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_014467235.1	s__Xenorhabdus indica	93.0107	1124	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_002632825.1	s__Xenorhabdus stockiae	83.9335	943	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.93	95.64	0.86	0.83	3	-
GCF_002632485.1	s__Xenorhabdus innexi	83.5836	933	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.1955	804	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	82.0864	773	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_900115195.1	s__Xenorhabdus japonica	81.9155	720	1369	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	81.9136	785	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	81.8337	775	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016306625.1	s__Xenorhabdus sp016306625	81.5526	793	1369	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:04,287] [INFO] GTDB search result was written to GCF_002632465.1_ASM263246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:04,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:04,290] [INFO] DFAST_QC result json was written to GCF_002632465.1_ASM263246v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:04,291] [INFO] DFAST_QC completed!
[2024-01-24 14:21:04,291] [INFO] Total running time: 0h1m19s