[2024-01-25 19:10:05,752] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference
[2024-01-25 19:10:06,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:06,929] [INFO] Task started: Prodigal
[2024-01-25 19:10:06,929] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e48db77-603a-4761-8ba6-64ae12d3e2b7/GCF_002127545.1_ASM212754v1_genomic.fna.gz | prodigal -d GCF_002127545.1_ASM212754v1_genomic.fna/cds.fna -a GCF_002127545.1_ASM212754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:16,449] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:16,449] [INFO] Task started: HMMsearch
[2024-01-25 19:10:16,449] [INFO] Running command: hmmsearch --tblout GCF_002127545.1_ASM212754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/reference_markers.hmm GCF_002127545.1_ASM212754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:16,693] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:16,694] [INFO] Found 6/6 markers.
[2024-01-25 19:10:16,726] [INFO] Query marker FASTA was written to GCF_002127545.1_ASM212754v1_genomic.fna/markers.fasta
[2024-01-25 19:10:16,726] [INFO] Task started: Blastn
[2024-01-25 19:10:16,726] [INFO] Running command: blastn -query GCF_002127545.1_ASM212754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/reference_markers.fasta -out GCF_002127545.1_ASM212754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:17,456] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:17,460] [INFO] Selected 16 target genomes.
[2024-01-25 19:10:17,460] [INFO] Target genome list was writen to GCF_002127545.1_ASM212754v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:17,475] [INFO] Task started: fastANI
[2024-01-25 19:10:17,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e48db77-603a-4761-8ba6-64ae12d3e2b7/GCF_002127545.1_ASM212754v1_genomic.fna.gz --refList GCF_002127545.1_ASM212754v1_genomic.fna/target_genomes.txt --output GCF_002127545.1_ASM212754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:32,691] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:32,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:32,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:32,702] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:32,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:32,702] [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 beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	100.0	1280	1286	95	conclusive
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	86.3286	1001	1286	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	85.3492	971	1286	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	84.1272	855	1286	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	83.9161	916	1286	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	83.9044	896	1286	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	83.8527	890	1286	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	83.8314	861	1286	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	83.8215	846	1286	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	83.2543	906	1286	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.1542	792	1286	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_000531455.1	290112	290112	type	True	82.1246	795	1286	95	below_threshold
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_002632585.1	290112	290112	type	True	82.0515	810	1286	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	79.0169	376	1286	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.7283	361	1286	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.6216	358	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:32,704] [INFO] DFAST Taxonomy check result was written to GCF_002127545.1_ASM212754v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:32,704] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:32,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:32,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/checkm_data
[2024-01-25 19:10:32,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:32,748] [INFO] Task started: CheckM
[2024-01-25 19:10:32,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002127545.1_ASM212754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002127545.1_ASM212754v1_genomic.fna/checkm_input GCF_002127545.1_ASM212754v1_genomic.fna/checkm_result
[2024-01-25 19:11:04,944] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:04,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:04,967] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:04,967] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:04,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002127545.1_ASM212754v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:04,967] [INFO] Task started: Blastn
[2024-01-25 19:11:04,967] [INFO] Running command: blastn -query GCF_002127545.1_ASM212754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg595bffea-8676-4c4e-9296-c62cb67e479e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002127545.1_ASM212754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:06,007] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:06,010] [INFO] Selected 13 target genomes.
[2024-01-25 19:11:06,010] [INFO] Target genome list was writen to GCF_002127545.1_ASM212754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:06,047] [INFO] Task started: fastANI
[2024-01-25 19:11:06,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e48db77-603a-4761-8ba6-64ae12d3e2b7/GCF_002127545.1_ASM212754v1_genomic.fna.gz --refList GCF_002127545.1_ASM212754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002127545.1_ASM212754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:19,199] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:19,208] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:19,208] [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_002127545.1	s__Xenorhabdus beddingii	100.0	1280	1286	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_001037465.1	s__Xenorhabdus khoisanae	86.3487	940	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632615.1	s__Xenorhabdus miraniensis	86.3361	1001	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_016306625.1	s__Xenorhabdus sp016306625	85.3376	971	1286	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	83.9108	895	1286	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	83.7911	848	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	83.7199	866	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_015163655.1	s__Xenorhabdus griffiniae	83.4801	852	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632725.1	s__Xenorhabdus hominickii	83.2508	907	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.1059	820	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_002632585.1	s__Xenorhabdus szentirmaii	82.0647	808	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.85	99.72	0.97	0.94	3	-
GCF_014467235.1	s__Xenorhabdus indica	81.3343	737	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_900094795.1	s__Kosakonia oryziphila	77.4591	124	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Kosakonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:19,211] [INFO] GTDB search result was written to GCF_002127545.1_ASM212754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:19,211] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:19,215] [INFO] DFAST_QC result json was written to GCF_002127545.1_ASM212754v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:19,215] [INFO] DFAST_QC completed!
[2024-01-25 19:11:19,215] [INFO] Total running time: 0h1m13s