[2024-01-24 12:06:34,873] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,881] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,881] [INFO] DQC Reference Directory: /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference
[2024-01-24 12:06:36,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:36,113] [INFO] Task started: Prodigal
[2024-01-24 12:06:36,113] [INFO] Running command: gunzip -c /var/lib/cwl/stge8d5b419-437f-431d-94eb-e9b0fe365a8d/GCF_028598495.1_ASM2859849v1_genomic.fna.gz | prodigal -d GCF_028598495.1_ASM2859849v1_genomic.fna/cds.fna -a GCF_028598495.1_ASM2859849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:48,415] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:48,416] [INFO] Task started: HMMsearch
[2024-01-24 12:06:48,416] [INFO] Running command: hmmsearch --tblout GCF_028598495.1_ASM2859849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/reference_markers.hmm GCF_028598495.1_ASM2859849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:48,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:48,738] [INFO] Found 6/6 markers.
[2024-01-24 12:06:48,781] [INFO] Query marker FASTA was written to GCF_028598495.1_ASM2859849v1_genomic.fna/markers.fasta
[2024-01-24 12:06:48,781] [INFO] Task started: Blastn
[2024-01-24 12:06:48,781] [INFO] Running command: blastn -query GCF_028598495.1_ASM2859849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/reference_markers.fasta -out GCF_028598495.1_ASM2859849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:49,608] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:49,612] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:49,613] [INFO] Target genome list was writen to GCF_028598495.1_ASM2859849v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:49,619] [INFO] Task started: fastANI
[2024-01-24 12:06:49,620] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d5b419-437f-431d-94eb-e9b0fe365a8d/GCF_028598495.1_ASM2859849v1_genomic.fna.gz --refList GCF_028598495.1_ASM2859849v1_genomic.fna/target_genomes.txt --output GCF_028598495.1_ASM2859849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:04,693] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:04,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:04,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:04,707] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:04,708] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:04,708] [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 ehlersii	strain=DSM 16337	GCA_002632445.1	290111	290111	type	True	91.9165	1073	1440	95	below_threshold
Xenorhabdus ehlersii	strain=DSM 16337	GCA_003610465.1	290111	290111	type	True	91.8576	1081	1440	95	below_threshold
Xenorhabdus thuongxuanensis	strain=30TX1	GCA_001908095.1	1873484	1873484	type	True	90.6326	1020	1440	95	below_threshold
Xenorhabdus eapokensis	strain=DL20	GCA_001908105.1	1873482	1873482	type	True	90.0633	998	1440	95	below_threshold
Xenorhabdus ishibashii	strain=DSM 22670	GCA_002632755.1	1034471	1034471	type	True	89.513	1011	1440	95	below_threshold
Xenorhabdus kozodoii	strain=DSM 17907	GCA_002632875.1	351676	351676	type	True	87.0254	986	1440	95	below_threshold
Xenorhabdus lircayensis	strain=VLS	GCA_016306625.1	2763499	2763499	type	True	84.4755	932	1440	95	below_threshold
Xenorhabdus bovienii	strain=T228	GCA_024721015.1	40576	40576	type	True	82.0031	767	1440	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	78.9428	384	1440	95	below_threshold
Enterobacter sichuanensis	strain=WCHECL1597	GCA_025002605.1	2071710	2071710	type	True	78.0278	111	1440	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	77.7593	173	1440	95	below_threshold
Enterobacter cloacae	strain=DSM 30054	GCA_021469225.1	550	550	type	True	77.7567	128	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:04,709] [INFO] DFAST Taxonomy check result was written to GCF_028598495.1_ASM2859849v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:04,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:04,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:04,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/checkm_data
[2024-01-24 12:07:04,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:04,757] [INFO] Task started: CheckM
[2024-01-24 12:07:04,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028598495.1_ASM2859849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028598495.1_ASM2859849v1_genomic.fna/checkm_input GCF_028598495.1_ASM2859849v1_genomic.fna/checkm_result
[2024-01-24 12:07:44,674] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:44,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:44,702] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:44,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:44,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028598495.1_ASM2859849v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:44,703] [INFO] Task started: Blastn
[2024-01-24 12:07:44,703] [INFO] Running command: blastn -query GCF_028598495.1_ASM2859849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge79c3faa-faeb-4ca2-96e6-cac8c7a11369/dqc_reference/reference_markers_gtdb.fasta -out GCF_028598495.1_ASM2859849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:45,777] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:45,781] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:45,781] [INFO] Target genome list was writen to GCF_028598495.1_ASM2859849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:45,793] [INFO] Task started: fastANI
[2024-01-24 12:07:45,793] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d5b419-437f-431d-94eb-e9b0fe365a8d/GCF_028598495.1_ASM2859849v1_genomic.fna.gz --refList GCF_028598495.1_ASM2859849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028598495.1_ASM2859849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:02,241] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:02,259] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:02,259] [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_015163655.1	s__Xenorhabdus griffiniae	96.8481	1085	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.94	99.94	0.96	0.96	2	conclusive
GCF_015163665.1	s__Xenorhabdus sp015163665	93.8049	1080	1440	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	91.8751	1079	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.74	99.51	0.89	0.84	3	-
GCF_001028135.1	s__Xenorhabdus griffiniae_A	90.9668	994	1440	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	90.6326	1020	1440	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	90.0717	999	1440	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	89.4846	1014	1440	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	84.063	953	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127545.1	s__Xenorhabdus beddingii	83.5343	890	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968175.1	s__Xenorhabdus poinarii	83.5192	810	1440	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	82.8549	929	1440	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	81.8671	844	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	97.70	96.37	0.89	0.86	7	-
GCF_014467235.1	s__Xenorhabdus indica	81.813	796	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Xenorhabdus	95.0	99.18	99.18	0.92	0.92	2	-
GCF_001984825.2	s__Enterobacter chengduensis	78.0695	111	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter	95.0	97.11	95.58	0.88	0.79	24	-
GCA_902706205.1	s__Scandinavium sp902706205	78.03	105	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Scandinavium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000734965.1	s__Trabulsiella guamensis	77.6985	109	1440	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Trabulsiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:02,261] [INFO] GTDB search result was written to GCF_028598495.1_ASM2859849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:02,261] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:02,265] [INFO] DFAST_QC result json was written to GCF_028598495.1_ASM2859849v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:02,265] [INFO] DFAST_QC completed!
[2024-01-24 12:08:02,265] [INFO] Total running time: 0h1m27s