[2024-01-25 17:42:50,685] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:42:50,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:42:50,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference
[2024-01-25 17:42:51,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:42:51,830] [INFO] Task started: Prodigal
[2024-01-25 17:42:51,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg414bf4ef-946d-4a94-b0f2-05091387186b/GCF_001908095.1_ASM190809v1_genomic.fna.gz | prodigal -d GCF_001908095.1_ASM190809v1_genomic.fna/cds.fna -a GCF_001908095.1_ASM190809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:01,704] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:01,704] [INFO] Task started: HMMsearch
[2024-01-25 17:43:01,704] [INFO] Running command: hmmsearch --tblout GCF_001908095.1_ASM190809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/reference_markers.hmm GCF_001908095.1_ASM190809v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:01,970] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:01,971] [INFO] Found 6/6 markers.
[2024-01-25 17:43:02,002] [INFO] Query marker FASTA was written to GCF_001908095.1_ASM190809v1_genomic.fna/markers.fasta
[2024-01-25 17:43:02,002] [INFO] Task started: Blastn
[2024-01-25 17:43:02,002] [INFO] Running command: blastn -query GCF_001908095.1_ASM190809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/reference_markers.fasta -out GCF_001908095.1_ASM190809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:02,736] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:02,739] [INFO] Selected 11 target genomes.
[2024-01-25 17:43:02,740] [INFO] Target genome list was writen to GCF_001908095.1_ASM190809v1_genomic.fna/target_genomes.txt
[2024-01-25 17:43:02,749] [INFO] Task started: fastANI
[2024-01-25 17:43:02,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg414bf4ef-946d-4a94-b0f2-05091387186b/GCF_001908095.1_ASM190809v1_genomic.fna.gz --refList GCF_001908095.1_ASM190809v1_genomic.fna/target_genomes.txt --output GCF_001908095.1_ASM190809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:43:13,709] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:13,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:43:13,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:43:13,717] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:43:13,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:43:13,717] [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 thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	100.0	1261	1265	95	conclusive
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	93.5953	1021	1265	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	93.5661	1030	1265	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	93.1087	967	1265	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	92.0231	966	1265	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	87.4726	941	1265	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.7108	884	1265	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.978	758	1265	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	79.0868	366	1265	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.2187	103	1265	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	77.9091	163	1265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:43:13,719] [INFO] DFAST Taxonomy check result was written to GCF_001908095.1_ASM190809v1_genomic.fna/tc_result.tsv
[2024-01-25 17:43:13,720] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:43:13,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:43:13,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/checkm_data
[2024-01-25 17:43:13,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:43:13,761] [INFO] Task started: CheckM
[2024-01-25 17:43:13,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001908095.1_ASM190809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001908095.1_ASM190809v1_genomic.fna/checkm_input GCF_001908095.1_ASM190809v1_genomic.fna/checkm_result
[2024-01-25 17:43:46,967] [INFO] Task succeeded: CheckM
[2024-01-25 17:43:46,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:43:46,987] [INFO] ===== Completeness check finished =====
[2024-01-25 17:43:46,988] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:43:46,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001908095.1_ASM190809v1_genomic.fna/markers.fasta)
[2024-01-25 17:43:46,988] [INFO] Task started: Blastn
[2024-01-25 17:43:46,988] [INFO] Running command: blastn -query GCF_001908095.1_ASM190809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a2d7945-70bb-4bef-be11-51c6a75096d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001908095.1_ASM190809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:43:48,111] [INFO] Task succeeded: Blastn
[2024-01-25 17:43:48,113] [INFO] Selected 6 target genomes.
[2024-01-25 17:43:48,114] [INFO] Target genome list was writen to GCF_001908095.1_ASM190809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:43:48,125] [INFO] Task started: fastANI
[2024-01-25 17:43:48,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg414bf4ef-946d-4a94-b0f2-05091387186b/GCF_001908095.1_ASM190809v1_genomic.fna.gz --refList GCF_001908095.1_ASM190809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001908095.1_ASM190809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:55,006] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:55,012] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:55,012] [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_001908095.1	s__Xenorhabdus thuongxuanensis	100.0	1259	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610465.1	s__Xenorhabdus ehlersii	93.5965	1028	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_001908105.1	s__Xenorhabdus eapokensis	93.0949	970	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632755.1	s__Xenorhabdus ishibashii	92.0236	966	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163665.1	s__Xenorhabdus sp015163665	91.3054	983	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015163655.1	s__Xenorhabdus griffiniae	90.4602	951	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:55,014] [INFO] GTDB search result was written to GCF_001908095.1_ASM190809v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:55,015] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:55,017] [INFO] DFAST_QC result json was written to GCF_001908095.1_ASM190809v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:55,017] [INFO] DFAST_QC completed!
[2024-01-25 17:43:55,017] [INFO] Total running time: 0h1m4s