[2024-01-24 10:57:36,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:36,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:36,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference
[2024-01-24 10:57:37,439] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:37,440] [INFO] Task started: Prodigal
[2024-01-24 10:57:37,440] [INFO] Running command: gunzip -c /var/lib/cwl/stge9410944-b0f6-4105-90ac-681dee349006/GCF_002632755.1_ASM263275v1_genomic.fna.gz | prodigal -d GCF_002632755.1_ASM263275v1_genomic.fna/cds.fna -a GCF_002632755.1_ASM263275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:47,038] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:47,038] [INFO] Task started: HMMsearch
[2024-01-24 10:57:47,039] [INFO] Running command: hmmsearch --tblout GCF_002632755.1_ASM263275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/reference_markers.hmm GCF_002632755.1_ASM263275v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:47,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:47,307] [INFO] Found 6/6 markers.
[2024-01-24 10:57:47,339] [INFO] Query marker FASTA was written to GCF_002632755.1_ASM263275v1_genomic.fna/markers.fasta
[2024-01-24 10:57:47,340] [INFO] Task started: Blastn
[2024-01-24 10:57:47,340] [INFO] Running command: blastn -query GCF_002632755.1_ASM263275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/reference_markers.fasta -out GCF_002632755.1_ASM263275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:48,116] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:48,120] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:48,120] [INFO] Target genome list was writen to GCF_002632755.1_ASM263275v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:48,125] [INFO] Task started: fastANI
[2024-01-24 10:57:48,125] [INFO] Running command: fastANI --query /var/lib/cwl/stge9410944-b0f6-4105-90ac-681dee349006/GCF_002632755.1_ASM263275v1_genomic.fna.gz --refList GCF_002632755.1_ASM263275v1_genomic.fna/target_genomes.txt --output GCF_002632755.1_ASM263275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:59,706] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:59,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:59,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:59,724] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:59,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:59,724] [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 ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	100.0	1276	1285	95	conclusive
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	93.1365	1012	1285	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	92.2135	949	1285	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	91.8373	1016	1285	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	91.6608	1009	1285	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	87.0685	989	1285	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.6663	875	1285	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.0678	732	1285	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	79.6035	114	1285	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.9327	362	1285	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	77.8612	180	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:59,727] [INFO] DFAST Taxonomy check result was written to GCF_002632755.1_ASM263275v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:59,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:59,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:59,728] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/checkm_data
[2024-01-24 10:57:59,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:59,770] [INFO] Task started: CheckM
[2024-01-24 10:57:59,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632755.1_ASM263275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632755.1_ASM263275v1_genomic.fna/checkm_input GCF_002632755.1_ASM263275v1_genomic.fna/checkm_result
[2024-01-24 10:58:33,590] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:33,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,613] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:33,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:33,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632755.1_ASM263275v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:33,614] [INFO] Task started: Blastn
[2024-01-24 10:58:33,615] [INFO] Running command: blastn -query GCF_002632755.1_ASM263275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4359d7e8-5552-41ce-85d5-455c9dc5ad9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632755.1_ASM263275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:34,870] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:34,874] [INFO] Selected 8 target genomes.
[2024-01-24 10:58:34,875] [INFO] Target genome list was writen to GCF_002632755.1_ASM263275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:34,881] [INFO] Task started: fastANI
[2024-01-24 10:58:34,881] [INFO] Running command: fastANI --query /var/lib/cwl/stge9410944-b0f6-4105-90ac-681dee349006/GCF_002632755.1_ASM263275v1_genomic.fna.gz --refList GCF_002632755.1_ASM263275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632755.1_ASM263275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:44,454] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:44,462] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:44,462] [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_002632755.1	s__Xenorhabdus ishibashii	100.0	1276	1285	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_001908105.1	s__Xenorhabdus eapokensis	93.163	1005	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	92.2099	949	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610465.1	s__Xenorhabdus ehlersii	91.7602	1018	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_015163665.1	s__Xenorhabdus sp015163665	90.0022	980	1285	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	89.5805	938	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	89.2606	949	1285	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_002632875.1	s__Xenorhabdus kozodoii	87.0634	988	1285	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 10:58:44,464] [INFO] GTDB search result was written to GCF_002632755.1_ASM263275v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:44,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:44,468] [INFO] DFAST_QC result json was written to GCF_002632755.1_ASM263275v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:44,468] [INFO] DFAST_QC completed!
[2024-01-24 10:58:44,468] [INFO] Total running time: 0h1m8s