[2024-01-24 14:46:54,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:54,736] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:54,736] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference
[2024-01-24 14:46:56,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:56,060] [INFO] Task started: Prodigal
[2024-01-24 14:46:56,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d6cfcd5-11cd-4d71-b507-0929d5549aec/GCF_026421305.1_ASM2642130v1_genomic.fna.gz | prodigal -d GCF_026421305.1_ASM2642130v1_genomic.fna/cds.fna -a GCF_026421305.1_ASM2642130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:11,228] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:11,228] [INFO] Task started: HMMsearch
[2024-01-24 14:47:11,228] [INFO] Running command: hmmsearch --tblout GCF_026421305.1_ASM2642130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/reference_markers.hmm GCF_026421305.1_ASM2642130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:11,561] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:11,563] [INFO] Found 6/6 markers.
[2024-01-24 14:47:11,605] [INFO] Query marker FASTA was written to GCF_026421305.1_ASM2642130v1_genomic.fna/markers.fasta
[2024-01-24 14:47:11,606] [INFO] Task started: Blastn
[2024-01-24 14:47:11,606] [INFO] Running command: blastn -query GCF_026421305.1_ASM2642130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/reference_markers.fasta -out GCF_026421305.1_ASM2642130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:12,729] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:12,733] [INFO] Selected 9 target genomes.
[2024-01-24 14:47:12,733] [INFO] Target genome list was writen to GCF_026421305.1_ASM2642130v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:12,737] [INFO] Task started: fastANI
[2024-01-24 14:47:12,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6cfcd5-11cd-4d71-b507-0929d5549aec/GCF_026421305.1_ASM2642130v1_genomic.fna.gz --refList GCF_026421305.1_ASM2642130v1_genomic.fna/target_genomes.txt --output GCF_026421305.1_ASM2642130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:22,665] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:22,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:22,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:22,674] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:22,674] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:22,674] [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
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	83.4016	982	1474	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	83.1608	951	1474	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	83.1504	950	1474	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	83.1471	961	1474	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	83.0321	793	1474	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	80.6502	598	1474	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.1087	636	1474	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.9018	558	1474	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	78.1411	260	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:22,676] [INFO] DFAST Taxonomy check result was written to GCF_026421305.1_ASM2642130v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:22,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:22,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:22,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/checkm_data
[2024-01-24 14:47:22,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:22,723] [INFO] Task started: CheckM
[2024-01-24 14:47:22,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026421305.1_ASM2642130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026421305.1_ASM2642130v1_genomic.fna/checkm_input GCF_026421305.1_ASM2642130v1_genomic.fna/checkm_result
[2024-01-24 14:48:11,632] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:11,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:11,656] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:11,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:11,657] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026421305.1_ASM2642130v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:11,657] [INFO] Task started: Blastn
[2024-01-24 14:48:11,658] [INFO] Running command: blastn -query GCF_026421305.1_ASM2642130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe38a3ba-8000-438a-b2b0-e31882f2098e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026421305.1_ASM2642130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:13,563] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:13,567] [INFO] Selected 13 target genomes.
[2024-01-24 14:48:13,567] [INFO] Target genome list was writen to GCF_026421305.1_ASM2642130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:13,578] [INFO] Task started: fastANI
[2024-01-24 14:48:13,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6cfcd5-11cd-4d71-b507-0929d5549aec/GCF_026421305.1_ASM2642130v1_genomic.fna.gz --refList GCF_026421305.1_ASM2642130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026421305.1_ASM2642130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:29,992] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:30,008] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:48:30,009] [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_003201105.1	s__Dyella jiangningensis_B	83.7471	975	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000725385.1	s__Dyella japonica_C	83.5438	1006	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014297575.1	s__Dyella sp014297575	83.4219	979	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016905005.1	s__Dyella kyungheensis	83.1619	948	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296575.1	s__Dyella sp004296575	83.1524	959	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351225.1	s__Dyella solisilvae	83.1401	952	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003264855.1	s__Dyella jiangningensis_C	83.1279	953	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010355.1	s__Dyella japonica	83.0509	791	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121485.1	s__Dyella sp003121485	83.041	933	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	83.0124	929	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688835.1	s__Dyella sp003688835	82.9225	970	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000632805.1	s__Dyella jiangningensis	82.9093	926	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002878475.1	s__Dyella sp002878475	82.6113	946	1474	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:30,011] [INFO] GTDB search result was written to GCF_026421305.1_ASM2642130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:30,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:30,016] [INFO] DFAST_QC result json was written to GCF_026421305.1_ASM2642130v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:30,016] [INFO] DFAST_QC completed!
[2024-01-24 14:48:30,017] [INFO] Total running time: 0h1m35s