[2024-01-24 11:51:19,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,494] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,494] [INFO] DQC Reference Directory: /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference
[2024-01-24 11:51:20,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,697] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,697] [INFO] Running command: gunzip -c /var/lib/cwl/stge69c2cc2-39b1-40b8-8b7e-e9d5906df530/GCF_014467235.1_ASM1446723v1_genomic.fna.gz | prodigal -d GCF_014467235.1_ASM1446723v1_genomic.fna/cds.fna -a GCF_014467235.1_ASM1446723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:33,960] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:33,961] [INFO] Task started: HMMsearch
[2024-01-24 11:51:33,961] [INFO] Running command: hmmsearch --tblout GCF_014467235.1_ASM1446723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/reference_markers.hmm GCF_014467235.1_ASM1446723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:34,248] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:34,250] [INFO] Found 6/6 markers.
[2024-01-24 11:51:34,291] [INFO] Query marker FASTA was written to GCF_014467235.1_ASM1446723v1_genomic.fna/markers.fasta
[2024-01-24 11:51:34,292] [INFO] Task started: Blastn
[2024-01-24 11:51:34,292] [INFO] Running command: blastn -query GCF_014467235.1_ASM1446723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/reference_markers.fasta -out GCF_014467235.1_ASM1446723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,034] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:35,034] [INFO] Target genome list was writen to GCF_014467235.1_ASM1446723v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,067] [INFO] Task started: fastANI
[2024-01-24 11:51:35,068] [INFO] Running command: fastANI --query /var/lib/cwl/stge69c2cc2-39b1-40b8-8b7e-e9d5906df530/GCF_014467235.1_ASM1446723v1_genomic.fna.gz --refList GCF_014467235.1_ASM1446723v1_genomic.fna/target_genomes.txt --output GCF_014467235.1_ASM1446723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:48,815] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:48,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:48,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:48,828] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:48,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:48,828] [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 indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	100.0	1433	1465	95	conclusive
Xenorhabdus budapestensis	strain=DSM 16342	GCA_002632465.1	290110	290110	type	True	92.9655	1126	1465	95	below_threshold
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	92.7977	1118	1465	95	below_threshold
Xenorhabdus stockiae	strain=DSM 17904	GCA_002632825.1	351614	351614	type	True	83.747	989	1465	95	below_threshold
Xenorhabdus innexi	strain=DSM 16336	GCA_002632485.1	290109	290109	type	True	83.3821	940	1465	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	81.9029	835	1465	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.8937	751	1465	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	81.4722	806	1465	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	79.0326	387	1465	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	79.0004	352	1465	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	78.854	378	1465	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.7806	389	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:48,830] [INFO] DFAST Taxonomy check result was written to GCF_014467235.1_ASM1446723v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:48,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:48,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:48,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/checkm_data
[2024-01-24 11:51:48,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:48,874] [INFO] Task started: CheckM
[2024-01-24 11:51:48,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014467235.1_ASM1446723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014467235.1_ASM1446723v1_genomic.fna/checkm_input GCF_014467235.1_ASM1446723v1_genomic.fna/checkm_result
[2024-01-24 11:52:33,720] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:33,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:33,745] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:33,745] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:33,745] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014467235.1_ASM1446723v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:33,746] [INFO] Task started: Blastn
[2024-01-24 11:52:33,746] [INFO] Running command: blastn -query GCF_014467235.1_ASM1446723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ee2329-e38c-4e7c-b49e-4c333abb224d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014467235.1_ASM1446723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:34,690] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:34,693] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:34,693] [INFO] Target genome list was writen to GCF_014467235.1_ASM1446723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:34,704] [INFO] Task started: fastANI
[2024-01-24 11:52:34,704] [INFO] Running command: fastANI --query /var/lib/cwl/stge69c2cc2-39b1-40b8-8b7e-e9d5906df530/GCF_014467235.1_ASM1446723v1_genomic.fna.gz --refList GCF_014467235.1_ASM1446723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014467235.1_ASM1446723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:48,539] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:48,551] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:48,552] [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_014467235.1	s__Xenorhabdus indica	100.0	1436	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	conclusive
GCF_002632465.1	s__Xenorhabdus budapestensis	92.9537	1128	1465	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	92.7595	1121	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_002632825.1	s__Xenorhabdus stockiae	83.7566	989	1465	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	83.4035	942	1465	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	82.0073	822	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_001037465.1	s__Xenorhabdus khoisanae	81.8906	804	1465	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	81.876	838	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	81.8662	771	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	81.8372	780	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_015163665.1	s__Xenorhabdus sp015163665	81.7397	790	1465	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	81.4667	807	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127545.1	s__Xenorhabdus beddingii	81.4191	742	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968175.1	s__Xenorhabdus poinarii	80.9152	655	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.71	96.71	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:48,553] [INFO] GTDB search result was written to GCF_014467235.1_ASM1446723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:48,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:48,558] [INFO] DFAST_QC result json was written to GCF_014467235.1_ASM1446723v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:48,558] [INFO] DFAST_QC completed!
[2024-01-24 11:52:48,558] [INFO] Total running time: 0h1m29s