[2024-01-24 15:03:29,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:29,243] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:29,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference
[2024-01-24 15:03:30,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:30,493] [INFO] Task started: Prodigal
[2024-01-24 15:03:30,493] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b43e283-a716-4e0f-bd24-592266ef01a5/GCF_002632875.1_ASM263287v1_genomic.fna.gz | prodigal -d GCF_002632875.1_ASM263287v1_genomic.fna/cds.fna -a GCF_002632875.1_ASM263287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:42,287] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:42,287] [INFO] Task started: HMMsearch
[2024-01-24 15:03:42,287] [INFO] Running command: hmmsearch --tblout GCF_002632875.1_ASM263287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/reference_markers.hmm GCF_002632875.1_ASM263287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:42,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:42,531] [INFO] Found 6/6 markers.
[2024-01-24 15:03:42,567] [INFO] Query marker FASTA was written to GCF_002632875.1_ASM263287v1_genomic.fna/markers.fasta
[2024-01-24 15:03:42,568] [INFO] Task started: Blastn
[2024-01-24 15:03:42,568] [INFO] Running command: blastn -query GCF_002632875.1_ASM263287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/reference_markers.fasta -out GCF_002632875.1_ASM263287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:43,309] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:43,312] [INFO] Selected 13 target genomes.
[2024-01-24 15:03:43,313] [INFO] Target genome list was writen to GCF_002632875.1_ASM263287v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:43,318] [INFO] Task started: fastANI
[2024-01-24 15:03:43,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b43e283-a716-4e0f-bd24-592266ef01a5/GCF_002632875.1_ASM263287v1_genomic.fna.gz --refList GCF_002632875.1_ASM263287v1_genomic.fna/target_genomes.txt --output GCF_002632875.1_ASM263287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:57,399] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:57,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:57,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:57,413] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:57,413] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:57,413] [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 kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	100.0	1293	1323	95	conclusive
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	87.852	1016	1323	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	87.8309	1017	1323	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	87.4847	952	1323	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	87.2473	969	1323	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	87.1182	969	1323	95	below_threshold
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	85.9125	952	1323	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	85.9018	980	1323	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.9578	912	1323	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.0243	735	1323	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	78.8624	140	1323	95	below_threshold
Enterobacter hormaechei	strain=FDAARGOS 1433	GCA_019048245.1	158836	158836	suspected-type	True	78.5837	123	1323	95	below_threshold
Enterobacter wuhouensis	strain=WCHEW120002	GCA_004331265.1	2529381	2529381	type	True	77.9678	115	1323	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:57,415] [INFO] DFAST Taxonomy check result was written to GCF_002632875.1_ASM263287v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:57,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:57,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:57,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/checkm_data
[2024-01-24 15:03:57,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:57,462] [INFO] Task started: CheckM
[2024-01-24 15:03:57,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002632875.1_ASM263287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002632875.1_ASM263287v1_genomic.fna/checkm_input GCF_002632875.1_ASM263287v1_genomic.fna/checkm_result
[2024-01-24 15:04:36,842] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:36,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:36,861] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:36,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:36,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002632875.1_ASM263287v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:36,862] [INFO] Task started: Blastn
[2024-01-24 15:04:36,862] [INFO] Running command: blastn -query GCF_002632875.1_ASM263287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cd5d2a5-8c0b-4059-8765-5311bcfb5aba/dqc_reference/reference_markers_gtdb.fasta -out GCF_002632875.1_ASM263287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:37,863] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:37,867] [INFO] Selected 12 target genomes.
[2024-01-24 15:04:37,867] [INFO] Target genome list was writen to GCF_002632875.1_ASM263287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:37,875] [INFO] Task started: fastANI
[2024-01-24 15:04:37,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b43e283-a716-4e0f-bd24-592266ef01a5/GCF_002632875.1_ASM263287v1_genomic.fna.gz --refList GCF_002632875.1_ASM263287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002632875.1_ASM263287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:51,287] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:51,297] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:51,297] [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_002632875.1	s__Xenorhabdus kozodoii	100.0	1295	1323	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	87.8653	1015	1323	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	87.6095	977	1323	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	87.5213	962	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	87.4882	951	1323	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	87.2282	975	1323	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	87.2165	947	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632755.1	s__Xenorhabdus ishibashii	87.0975	969	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968195.1	s__Xenorhabdus doucetiae	85.8597	984	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002632615.1	s__Xenorhabdus miraniensis	83.8183	932	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_000973125.1	s__Xenorhabdus bovienii	82.0122	788	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_000027225.1	s__Xenorhabdus bovienii_C	81.8909	754	1323	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:51,299] [INFO] GTDB search result was written to GCF_002632875.1_ASM263287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:51,300] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:51,303] [INFO] DFAST_QC result json was written to GCF_002632875.1_ASM263287v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:51,303] [INFO] DFAST_QC completed!
[2024-01-24 15:04:51,304] [INFO] Total running time: 0h1m22s