[2024-01-24 15:18:23,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:23,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:23,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference
[2024-01-24 15:18:25,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,004] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,004] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0d5279d-5d1b-432d-b9e2-0d5e50dc7410/GCF_002632585.1_ASM263258v1_genomic.fna.gz | prodigal -d GCF_002632585.1_ASM263258v1_genomic.fna/cds.fna -a GCF_002632585.1_ASM263258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:46,432] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:46,433] [INFO] Task started: HMMsearch
[2024-01-24 15:18:46,433] [INFO] Running command: hmmsearch --tblout GCF_002632585.1_ASM263258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/reference_markers.hmm GCF_002632585.1_ASM263258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:46,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:46,783] [INFO] Found 6/6 markers.
[2024-01-24 15:18:46,828] [INFO] Query marker FASTA was written to GCF_002632585.1_ASM263258v1_genomic.fna/markers.fasta
[2024-01-24 15:18:46,829] [INFO] Task started: Blastn
[2024-01-24 15:18:46,829] [INFO] Running command: blastn -query GCF_002632585.1_ASM263258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/reference_markers.fasta -out GCF_002632585.1_ASM263258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:47,688] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:47,691] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:47,692] [INFO] Target genome list was writen to GCF_002632585.1_ASM263258v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:47,698] [INFO] Task started: fastANI
[2024-01-24 15:18:47,698] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d5279d-5d1b-432d-b9e2-0d5e50dc7410/GCF_002632585.1_ASM263258v1_genomic.fna.gz --refList GCF_002632585.1_ASM263258v1_genomic.fna/target_genomes.txt --output GCF_002632585.1_ASM263258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:06,091] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:06,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:06,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:06,110] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:06,110] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:06,110] [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 szentirmaii	strain=DSM 16338	GCA_002632585.1	290112	290112	type	True	99.9991	1633	1636	95	conclusive
Xenorhabdus szentirmaii	strain=DSM 16338	GCA_000531455.1	290112	290112	type	True	99.9365	1517	1636	95	conclusive
Xenorhabdus nematophila	strain=ATCC 19061	GCA_000252955.1	628	628	type	True	83.3662	895	1636	95	below_threshold
Xenorhabdus mauleonii	strain=DSM 17908	GCA_900113945.1	351675	351675	type	True	83.3276	973	1636	95	below_threshold
Xenorhabdus mauleonii	strain=DSM 17908	GCA_002632685.1	351675	351675	type	True	83.3224	983	1636	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.0599	911	1636	95	below_threshold
Xenorhabdus japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	82.2672	775	1636	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	82.138	912	1636	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	82.123	812	1636	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	82.0051	770	1636	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	81.9479	782	1636	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	81.7451	769	1636	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	81.1991	737	1636	95	below_threshold
Hafnia paralvei	strain=ATCC 29927	GCA_023698525.1	546367	546367	type	True	79.217	148	1636	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	78.662	355	1636	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.6512	376	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,112] [INFO] DFAST Taxonomy check result was written to GCF_002632585.1_ASM263258v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:06,113] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:06,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:06,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/checkm_data
[2024-01-24 15:19:06,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:06,164] [INFO] Task started: CheckM
[2024-01-24 15:19:06,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632585.1_ASM263258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632585.1_ASM263258v1_genomic.fna/checkm_input GCF_002632585.1_ASM263258v1_genomic.fna/checkm_result
[2024-01-24 15:20:10,458] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:10,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:10,480] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:10,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:10,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632585.1_ASM263258v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:10,481] [INFO] Task started: Blastn
[2024-01-24 15:20:10,481] [INFO] Running command: blastn -query GCF_002632585.1_ASM263258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf637841d-381f-4897-ad0b-cf0999c8d342/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632585.1_ASM263258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:11,674] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:11,678] [INFO] Selected 15 target genomes.
[2024-01-24 15:20:11,678] [INFO] Target genome list was writen to GCF_002632585.1_ASM263258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:11,689] [INFO] Task started: fastANI
[2024-01-24 15:20:11,689] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0d5279d-5d1b-432d-b9e2-0d5e50dc7410/GCF_002632585.1_ASM263258v1_genomic.fna.gz --refList GCF_002632585.1_ASM263258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632585.1_ASM263258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:27,121] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:27,137] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:27,138] [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_002632585.1	s__Xenorhabdus szentirmaii	99.9991	1634	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.85	99.72	0.97	0.94	3	conclusive
GCF_000252955.1	s__Xenorhabdus nematophila	83.3779	897	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.26	98.94	0.93	0.90	7	-
GCF_900113945.1	s__Xenorhabdus mauleonii	83.3362	970	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016306625.1	s__Xenorhabdus sp016306625	83.065	910	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115195.1	s__Xenorhabdus japonica	82.278	775	1636	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	82.1662	909	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_003610465.1	s__Xenorhabdus ehlersii	82.118	811	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_002127545.1	s__Xenorhabdus beddingii	82.1022	813	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001037465.1	s__Xenorhabdus khoisanae	82.0552	889	1636	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	82.0162	770	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001908105.1	s__Xenorhabdus eapokensis	81.8963	789	1636	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	81.7617	881	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	81.7408	766	1636	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	81.7381	779	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	81.7287	886	1636	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 15:20:27,140] [INFO] GTDB search result was written to GCF_002632585.1_ASM263258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:27,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:27,147] [INFO] DFAST_QC result json was written to GCF_002632585.1_ASM263258v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:27,147] [INFO] DFAST_QC completed!
[2024-01-24 15:20:27,147] [INFO] Total running time: 0h2m4s