[2024-01-24 13:41:40,359] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference
[2024-01-24 13:41:41,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,658] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,658] [INFO] Running command: gunzip -c /var/lib/cwl/stg19310b5d-e8b1-4918-a247-d9a63980c3b9/GCF_000429845.1_ASM42984v1_genomic.fna.gz | prodigal -d GCF_000429845.1_ASM42984v1_genomic.fna/cds.fna -a GCF_000429845.1_ASM42984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:57,635] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:57,635] [INFO] Task started: HMMsearch
[2024-01-24 13:41:57,636] [INFO] Running command: hmmsearch --tblout GCF_000429845.1_ASM42984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/reference_markers.hmm GCF_000429845.1_ASM42984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:57,904] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:57,906] [INFO] Found 6/6 markers.
[2024-01-24 13:41:57,948] [INFO] Query marker FASTA was written to GCF_000429845.1_ASM42984v1_genomic.fna/markers.fasta
[2024-01-24 13:41:57,949] [INFO] Task started: Blastn
[2024-01-24 13:41:57,949] [INFO] Running command: blastn -query GCF_000429845.1_ASM42984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/reference_markers.fasta -out GCF_000429845.1_ASM42984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,897] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,900] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:58,900] [INFO] Target genome list was writen to GCF_000429845.1_ASM42984v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:58,910] [INFO] Task started: fastANI
[2024-01-24 13:41:58,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg19310b5d-e8b1-4918-a247-d9a63980c3b9/GCF_000429845.1_ASM42984v1_genomic.fna.gz --refList GCF_000429845.1_ASM42984v1_genomic.fna/target_genomes.txt --output GCF_000429845.1_ASM42984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:15,141] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:15,141] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:15,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:15,157] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:15,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:15,158] [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
Comamonas phosphati	strain=CGMCC 1.12294	GCA_014637085.1	1211803	1211803	type	True	83.0441	778	1519	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	82.9722	961	1519	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	82.9489	946	1519	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	82.6667	868	1519	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_000964545.1	363952	363952	type	True	81.3405	781	1519	95	below_threshold
Comamonas testosteroni	strain=ATCC 11996	GCA_000241525.2	285	285	suspected-type	True	81.3051	786	1519	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001517325.1	363952	363952	type	True	81.2503	781	1519	95	below_threshold
Comamonas thiooxydans	strain=DSM 17888	GCA_001418295.1	363952	363952	type	True	81.2229	784	1519	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	81.1899	689	1519	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	81.0593	634	1519	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	80.4946	698	1519	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	79.9907	611	1519	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.8101	593	1519	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	79.7269	614	1519	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.2386	486	1519	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.6516	390	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,159] [INFO] DFAST Taxonomy check result was written to GCF_000429845.1_ASM42984v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:15,160] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:15,160] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:15,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/checkm_data
[2024-01-24 13:42:15,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:15,204] [INFO] Task started: CheckM
[2024-01-24 13:42:15,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429845.1_ASM42984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429845.1_ASM42984v1_genomic.fna/checkm_input GCF_000429845.1_ASM42984v1_genomic.fna/checkm_result
[2024-01-24 13:43:02,589] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:02,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:02,613] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:02,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:02,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429845.1_ASM42984v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:02,614] [INFO] Task started: Blastn
[2024-01-24 13:43:02,614] [INFO] Running command: blastn -query GCF_000429845.1_ASM42984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5618786-f98e-4373-aa5d-04837fb86f38/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429845.1_ASM42984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:04,485] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:04,489] [INFO] Selected 14 target genomes.
[2024-01-24 13:43:04,490] [INFO] Target genome list was writen to GCF_000429845.1_ASM42984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:04,542] [INFO] Task started: fastANI
[2024-01-24 13:43:04,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg19310b5d-e8b1-4918-a247-d9a63980c3b9/GCF_000429845.1_ASM42984v1_genomic.fna.gz --refList GCF_000429845.1_ASM42984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429845.1_ASM42984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:19,720] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:19,736] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:19,737] [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_000429845.1	s__Comamonas composti	100.0	1514	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001571325.1	s__Comamonas tsuruhatensis	83.1369	946	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	98.55	98.21	0.90	0.80	27	-
GCF_014637085.1	s__Comamonas phosphati	83.026	780	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598795.1	s__Comamonas acidovorans	82.917	950	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.4801	97.72	96.19	0.89	0.80	41	-
GCF_001544075.1	s__Comamonas terrae	82.6614	868	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236485.1	s__Comamonas sp019236485	82.3798	608	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461435.1	s__Comamonas terrigena	81.2131	686	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	97.97	95.46	0.95	0.91	7	-
GCF_000739875.1	s__Comamonas aquatica	81.0425	636	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	96.97	96.57	0.89	0.87	7	-
GCA_018242005.1	s__Alicycliphilus sp018242005	80.6793	590	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003755025.1	s__Diaphorobacter nitroreducens	80.6778	619	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Diaphorobacter	95.0	98.11	97.62	0.91	0.81	15	-
GCF_014204315.1	s__Comamonas konjaci_A	80.5653	707	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019186805.1	s__Comamonas sp019186805	80.5201	695	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727115.1	s__Comamonas testosteroni_E	80.4644	691	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207855.1	s__Comamonas odontotermitis	79.4732	527	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:19,739] [INFO] GTDB search result was written to GCF_000429845.1_ASM42984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:19,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:19,744] [INFO] DFAST_QC result json was written to GCF_000429845.1_ASM42984v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:19,744] [INFO] DFAST_QC completed!
[2024-01-24 13:43:19,744] [INFO] Total running time: 0h1m39s