[2024-01-24 11:35:10,367] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,369] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference
[2024-01-24 11:35:11,742] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:11,743] [INFO] Task started: Prodigal
[2024-01-24 11:35:11,743] [INFO] Running command: gunzip -c /var/lib/cwl/stg42d9bf23-16d2-47dc-a17d-f40a628d6cd0/GCF_002632485.1_ASM263248v1_genomic.fna.gz | prodigal -d GCF_002632485.1_ASM263248v1_genomic.fna/cds.fna -a GCF_002632485.1_ASM263248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:22,338] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:22,338] [INFO] Task started: HMMsearch
[2024-01-24 11:35:22,339] [INFO] Running command: hmmsearch --tblout GCF_002632485.1_ASM263248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/reference_markers.hmm GCF_002632485.1_ASM263248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:22,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:22,669] [INFO] Found 6/6 markers.
[2024-01-24 11:35:22,709] [INFO] Query marker FASTA was written to GCF_002632485.1_ASM263248v1_genomic.fna/markers.fasta
[2024-01-24 11:35:22,709] [INFO] Task started: Blastn
[2024-01-24 11:35:22,709] [INFO] Running command: blastn -query GCF_002632485.1_ASM263248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/reference_markers.fasta -out GCF_002632485.1_ASM263248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:23,493] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:23,498] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:23,498] [INFO] Target genome list was writen to GCF_002632485.1_ASM263248v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:23,504] [INFO] Task started: fastANI
[2024-01-24 11:35:23,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d9bf23-16d2-47dc-a17d-f40a628d6cd0/GCF_002632485.1_ASM263248v1_genomic.fna.gz --refList GCF_002632485.1_ASM263248v1_genomic.fna/target_genomes.txt --output GCF_002632485.1_ASM263248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:36,008] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:36,009] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:36,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:36,020] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:36,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:36,020] [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 innexi	strain=DSM 16336	GCA_002632485.1	290109	290109	type	True	100.0	1398	1401	95	conclusive
Xenorhabdus stockiae	strain=DSM 17904	GCA_002632825.1	351614	351614	type	True	87.8625	1084	1401	95	below_threshold
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	83.9932	939	1401	95	below_threshold
Xenorhabdus budapestensis	strain=DSM 16342	GCA_002632465.1	290110	290110	type	True	83.591	922	1401	95	below_threshold
Xenorhabdus indica	strain=DSM 17382	GCA_014467235.1	333964	333964	type	True	83.1967	952	1401	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.4246	719	1401	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	81.2787	724	1401	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	80.9319	681	1401	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.7194	339	1401	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.6955	353	1401	95	below_threshold
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	78.6526	352	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:36,023] [INFO] DFAST Taxonomy check result was written to GCF_002632485.1_ASM263248v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:36,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:36,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:36,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/checkm_data
[2024-01-24 11:35:36,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:36,088] [INFO] Task started: CheckM
[2024-01-24 11:35:36,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632485.1_ASM263248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632485.1_ASM263248v1_genomic.fna/checkm_input GCF_002632485.1_ASM263248v1_genomic.fna/checkm_result
[2024-01-24 11:36:14,618] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:14,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:14,639] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:14,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:14,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632485.1_ASM263248v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:14,641] [INFO] Task started: Blastn
[2024-01-24 11:36:14,641] [INFO] Running command: blastn -query GCF_002632485.1_ASM263248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3997e58-5ee2-4aae-95a4-aa8703aa5d30/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632485.1_ASM263248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:15,627] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:15,633] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:15,633] [INFO] Target genome list was writen to GCF_002632485.1_ASM263248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:15,642] [INFO] Task started: fastANI
[2024-01-24 11:36:15,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg42d9bf23-16d2-47dc-a17d-f40a628d6cd0/GCF_002632485.1_ASM263248v1_genomic.fna.gz --refList GCF_002632485.1_ASM263248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632485.1_ASM263248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:24,559] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:24,572] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:24,572] [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_002632485.1	s__Xenorhabdus innexi	100.0	1398	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.93	99.93	0.99	0.99	2	conclusive
GCF_002632825.1	s__Xenorhabdus stockiae	87.8432	1086	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.93	95.64	0.86	0.83	3	-
GCF_003386665.1	s__Xenorhabdus cabanillasii	83.9559	943	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_002632465.1	s__Xenorhabdus budapestensis	83.5913	924	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
GCF_014467235.1	s__Xenorhabdus indica	83.1874	952	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_000252955.1	s__Xenorhabdus nematophila	81.3584	704	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_016306625.1	s__Xenorhabdus sp016306625	81.2815	724	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113945.1	s__Xenorhabdus mauleonii	81.2034	702	1401	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:24,574] [INFO] GTDB search result was written to GCF_002632485.1_ASM263248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:24,575] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:24,578] [INFO] DFAST_QC result json was written to GCF_002632485.1_ASM263248v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:24,578] [INFO] DFAST_QC completed!
[2024-01-24 11:36:24,578] [INFO] Total running time: 0h1m14s