[2024-01-24 12:51:05,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,605] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference
[2024-01-24 12:51:06,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,831] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cadda38-e6d9-4511-94e6-3d870927d771/GCF_028598775.1_ASM2859877v1_genomic.fna.gz | prodigal -d GCF_028598775.1_ASM2859877v1_genomic.fna/cds.fna -a GCF_028598775.1_ASM2859877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:18,641] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:18,641] [INFO] Task started: HMMsearch
[2024-01-24 12:51:18,642] [INFO] Running command: hmmsearch --tblout GCF_028598775.1_ASM2859877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/reference_markers.hmm GCF_028598775.1_ASM2859877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:18,926] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:18,928] [INFO] Found 6/6 markers.
[2024-01-24 12:51:18,967] [INFO] Query marker FASTA was written to GCF_028598775.1_ASM2859877v1_genomic.fna/markers.fasta
[2024-01-24 12:51:18,967] [INFO] Task started: Blastn
[2024-01-24 12:51:18,967] [INFO] Running command: blastn -query GCF_028598775.1_ASM2859877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/reference_markers.fasta -out GCF_028598775.1_ASM2859877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:19,708] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:19,711] [INFO] Selected 20 target genomes.
[2024-01-24 12:51:19,712] [INFO] Target genome list was writen to GCF_028598775.1_ASM2859877v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:19,720] [INFO] Task started: fastANI
[2024-01-24 12:51:19,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cadda38-e6d9-4511-94e6-3d870927d771/GCF_028598775.1_ASM2859877v1_genomic.fna.gz --refList GCF_028598775.1_ASM2859877v1_genomic.fna/target_genomes.txt --output GCF_028598775.1_ASM2859877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:37,728] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:37,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:37,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:37,744] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:37,744] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:37,744] [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 bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	96.1948	1136	1505	95	conclusive
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	83.1767	959	1505	95	below_threshold
Xenorhabdus hominickii	strain=DSM 17903	GCA_002632725.1	351679	351679	type	True	82.6676	919	1505	95	below_threshold
Xenorhabdus miraniensis	strain=DSM 17902	GCA_002632615.1	351674	351674	type	True	82.6254	931	1505	95	below_threshold
Xenorhabdus beddingii	strain=DSM 4764	GCA_002127545.1	40578	40578	type	True	82.4045	807	1505	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	82.3288	813	1505	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	82.2798	812	1505	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	82.1145	767	1505	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	81.9861	786	1505	95	below_threshold
Xenorhabdus cabanillasii	strain=DSM 17905	GCA_003386665.1	351673	351673	type	True	81.9529	832	1505	95	below_threshold
Xenorhabdus doucetiae	strain=DSM 17909	GCA_008124675.1	351671	351671	type	True	81.9136	778	1505	95	below_threshold
Xenorhabdus doucetiae	strain=FRM16	GCA_000968195.1	351671	351671	type	True	81.8195	797	1505	95	below_threshold
Xenorhabdus stockiae	strain=DSM 17904	GCA_002632825.1	351614	351614	type	True	81.4999	748	1505	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.8746	406	1505	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	78.7655	410	1505	95	below_threshold
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	78.6872	387	1505	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	77.4758	168	1505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:37,745] [INFO] DFAST Taxonomy check result was written to GCF_028598775.1_ASM2859877v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:37,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:37,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:37,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/checkm_data
[2024-01-24 12:51:37,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:37,792] [INFO] Task started: CheckM
[2024-01-24 12:51:37,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028598775.1_ASM2859877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028598775.1_ASM2859877v1_genomic.fna/checkm_input GCF_028598775.1_ASM2859877v1_genomic.fna/checkm_result
[2024-01-24 12:52:17,393] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:17,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:17,440] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:17,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:17,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028598775.1_ASM2859877v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:17,441] [INFO] Task started: Blastn
[2024-01-24 12:52:17,442] [INFO] Running command: blastn -query GCF_028598775.1_ASM2859877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg737b0a38-da46-4237-b19b-4b8a98a700fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_028598775.1_ASM2859877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:18,391] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:18,395] [INFO] Selected 14 target genomes.
[2024-01-24 12:52:18,395] [INFO] Target genome list was writen to GCF_028598775.1_ASM2859877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:18,441] [INFO] Task started: fastANI
[2024-01-24 12:52:18,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cadda38-e6d9-4511-94e6-3d870927d771/GCF_028598775.1_ASM2859877v1_genomic.fna.gz --refList GCF_028598775.1_ASM2859877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028598775.1_ASM2859877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:32,071] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:32,084] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:32,084] [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_000973125.1	s__Xenorhabdus bovienii	95.9294	1229	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	conclusive
GCF_000027225.1	s__Xenorhabdus bovienii_C	94.1742	1129	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.07	95.57	0.88	0.81	4	-
GCF_016306625.1	s__Xenorhabdus sp016306625	83.1732	957	1505	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	82.7255	845	1505	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	82.6446	924	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.90	99.90	0.96	0.96	2	-
GCF_002632615.1	s__Xenorhabdus miraniensis	82.6091	934	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	95.51	95.51	0.84	0.84	2	-
GCF_002127545.1	s__Xenorhabdus beddingii	82.4103	808	1505	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	82.319	814	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_002127535.1	s__Xenorhabdus vietnamensis	82.1654	889	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002632465.1	s__Xenorhabdus budapestensis	82.0599	821	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.99	98.99	0.92	0.92	2	-
GCF_001908095.1	s__Xenorhabdus thuongxuanensis	81.987	785	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386665.1	s__Xenorhabdus cabanillasii	81.9855	828	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	98.80	98.76	0.86	0.85	3	-
GCF_000968195.1	s__Xenorhabdus doucetiae	81.8436	793	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002632825.1	s__Xenorhabdus stockiae	81.4838	750	1505	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	96.93	95.64	0.86	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:32,086] [INFO] GTDB search result was written to GCF_028598775.1_ASM2859877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:32,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:32,091] [INFO] DFAST_QC result json was written to GCF_028598775.1_ASM2859877v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:32,091] [INFO] DFAST_QC completed!
[2024-01-24 12:52:32,091] [INFO] Total running time: 0h1m26s