[2024-01-24 11:27:04,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference
[2024-01-24 11:27:06,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:06,201] [INFO] Task started: Prodigal
[2024-01-24 11:27:06,202] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc659b52-e6b0-47ca-8fea-2aaaff5d5588/GCF_028598555.1_ASM2859855v1_genomic.fna.gz | prodigal -d GCF_028598555.1_ASM2859855v1_genomic.fna/cds.fna -a GCF_028598555.1_ASM2859855v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:16,785] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:16,785] [INFO] Task started: HMMsearch
[2024-01-24 11:27:16,786] [INFO] Running command: hmmsearch --tblout GCF_028598555.1_ASM2859855v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/reference_markers.hmm GCF_028598555.1_ASM2859855v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:17,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:17,093] [INFO] Found 6/6 markers.
[2024-01-24 11:27:17,131] [INFO] Query marker FASTA was written to GCF_028598555.1_ASM2859855v1_genomic.fna/markers.fasta
[2024-01-24 11:27:17,132] [INFO] Task started: Blastn
[2024-01-24 11:27:17,132] [INFO] Running command: blastn -query GCF_028598555.1_ASM2859855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/reference_markers.fasta -out GCF_028598555.1_ASM2859855v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:17,871] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:17,875] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:17,875] [INFO] Target genome list was writen to GCF_028598555.1_ASM2859855v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:17,891] [INFO] Task started: fastANI
[2024-01-24 11:27:17,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc659b52-e6b0-47ca-8fea-2aaaff5d5588/GCF_028598555.1_ASM2859855v1_genomic.fna.gz --refList GCF_028598555.1_ASM2859855v1_genomic.fna/target_genomes.txt --output GCF_028598555.1_ASM2859855v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:36,232] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:36,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:36,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:36,248] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:36,248] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:36,249] [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 japonica	strain=DSM 16522	GCA_900115195.1	53341	53341	type	True	93.2049	1000	1397	95	below_threshold
Xenorhabdus vietnamensis	strain=DSM 22392	GCA_002127535.1	351656	351656	type	True	90.4713	1108	1397	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	87.0944	1009	1397	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	87.087	1023	1397	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	86.6843	955	1397	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	86.5272	942	1397	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	85.6338	963	1397	95	below_threshold
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	85.6021	950	1397	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	85.4231	1009	1397	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	85.4222	976	1397	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	84.8456	1022	1397	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	84.111	989	1397	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.5201	829	1397	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	79.1033	387	1397	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.8118	378	1397	95	below_threshold
Pluralibacter gergoviae	strain=NBRC 105706	GCA_001598855.1	61647	61647	type	True	78.3549	83	1397	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	77.8777	164	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:36,250] [INFO] DFAST Taxonomy check result was written to GCF_028598555.1_ASM2859855v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:36,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:36,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:36,251] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/checkm_data
[2024-01-24 11:27:36,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:36,298] [INFO] Task started: CheckM
[2024-01-24 11:27:36,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028598555.1_ASM2859855v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028598555.1_ASM2859855v1_genomic.fna/checkm_input GCF_028598555.1_ASM2859855v1_genomic.fna/checkm_result
[2024-01-24 11:28:12,892] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:12,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:12,912] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:12,912] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:12,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028598555.1_ASM2859855v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:12,913] [INFO] Task started: Blastn
[2024-01-24 11:28:12,913] [INFO] Running command: blastn -query GCF_028598555.1_ASM2859855v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d23788a-2bd4-4191-8049-bcba8c008561/dqc_reference/reference_markers_gtdb.fasta -out GCF_028598555.1_ASM2859855v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:13,902] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:13,906] [INFO] Selected 16 target genomes.
[2024-01-24 11:28:13,906] [INFO] Target genome list was writen to GCF_028598555.1_ASM2859855v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:13,922] [INFO] Task started: fastANI
[2024-01-24 11:28:13,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc659b52-e6b0-47ca-8fea-2aaaff5d5588/GCF_028598555.1_ASM2859855v1_genomic.fna.gz --refList GCF_028598555.1_ASM2859855v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028598555.1_ASM2859855v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:29,823] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:29,838] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:28:29,839] [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_900115195.1	s__Xenorhabdus japonica	93.2125	999	1397	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	90.4537	1110	1397	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	87.0987	1020	1397	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	86.5094	983	1397	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	86.5032	944	1397	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	86.488	949	1397	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	86.1766	951	1397	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	86.1644	944	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002632875.1	s__Xenorhabdus kozodoii	85.6302	962	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016306625.1	s__Xenorhabdus sp016306625	85.429	1009	1397	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	85.4231	976	1397	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	84.8411	1024	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_000968175.1	s__Xenorhabdus poinarii	84.6788	873	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.71	96.71	0.87	0.87	2	-
GCF_002632725.1	s__Xenorhabdus hominickii	84.1108	987	1397	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	82.2625	903	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_002632465.1	s__Xenorhabdus budapestensis	81.9268	802	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:29,840] [INFO] GTDB search result was written to GCF_028598555.1_ASM2859855v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:29,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:29,844] [INFO] DFAST_QC result json was written to GCF_028598555.1_ASM2859855v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:29,844] [INFO] DFAST_QC completed!
[2024-01-24 11:28:29,844] [INFO] Total running time: 0h1m25s