[2024-01-25 19:47:05,489] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:05,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:05,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference
[2024-01-25 19:47:06,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:06,631] [INFO] Task started: Prodigal
[2024-01-25 19:47:06,632] [INFO] Running command: gunzip -c /var/lib/cwl/stg634222aa-004d-47d8-9a39-a11a6b0ccb83/GCF_014837235.1_ASM1483723v1_genomic.fna.gz | prodigal -d GCF_014837235.1_ASM1483723v1_genomic.fna/cds.fna -a GCF_014837235.1_ASM1483723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:18,316] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:18,317] [INFO] Task started: HMMsearch
[2024-01-25 19:47:18,317] [INFO] Running command: hmmsearch --tblout GCF_014837235.1_ASM1483723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/reference_markers.hmm GCF_014837235.1_ASM1483723v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:18,553] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:18,554] [INFO] Found 6/6 markers.
[2024-01-25 19:47:18,585] [INFO] Query marker FASTA was written to GCF_014837235.1_ASM1483723v1_genomic.fna/markers.fasta
[2024-01-25 19:47:18,585] [INFO] Task started: Blastn
[2024-01-25 19:47:18,586] [INFO] Running command: blastn -query GCF_014837235.1_ASM1483723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/reference_markers.fasta -out GCF_014837235.1_ASM1483723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:19,396] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:19,399] [INFO] Selected 17 target genomes.
[2024-01-25 19:47:19,399] [INFO] Target genome list was writen to GCF_014837235.1_ASM1483723v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:19,407] [INFO] Task started: fastANI
[2024-01-25 19:47:19,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg634222aa-004d-47d8-9a39-a11a6b0ccb83/GCF_014837235.1_ASM1483723v1_genomic.fna.gz --refList GCF_014837235.1_ASM1483723v1_genomic.fna/target_genomes.txt --output GCF_014837235.1_ASM1483723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:34,800] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:34,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:34,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:34,812] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:34,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:34,812] [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
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	100.0	1104	1104	95	conclusive
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	83.9491	649	1104	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	83.3205	662	1104	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	80.1063	440	1104	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.8113	531	1104	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.6793	489	1104	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.6522	485	1104	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.5987	463	1104	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.4271	430	1104	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	79.262	462	1104	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	79.2196	442	1104	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	79.1315	450	1104	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	79.052	393	1104	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.9614	384	1104	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.8722	437	1104	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	78.765	361	1104	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	78.6744	420	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:34,813] [INFO] DFAST Taxonomy check result was written to GCF_014837235.1_ASM1483723v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:34,814] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:34,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:34,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/checkm_data
[2024-01-25 19:47:34,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:34,852] [INFO] Task started: CheckM
[2024-01-25 19:47:34,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837235.1_ASM1483723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837235.1_ASM1483723v1_genomic.fna/checkm_input GCF_014837235.1_ASM1483723v1_genomic.fna/checkm_result
[2024-01-25 19:49:16,887] [INFO] Task succeeded: CheckM
[2024-01-25 19:49:16,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:49:16,911] [INFO] ===== Completeness check finished =====
[2024-01-25 19:49:16,912] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:49:16,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837235.1_ASM1483723v1_genomic.fna/markers.fasta)
[2024-01-25 19:49:16,913] [INFO] Task started: Blastn
[2024-01-25 19:49:16,913] [INFO] Running command: blastn -query GCF_014837235.1_ASM1483723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb277bb9e-e918-4e20-a917-324a26bc5be5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837235.1_ASM1483723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:49:18,456] [INFO] Task succeeded: Blastn
[2024-01-25 19:49:18,459] [INFO] Selected 17 target genomes.
[2024-01-25 19:49:18,459] [INFO] Target genome list was writen to GCF_014837235.1_ASM1483723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:49:18,516] [INFO] Task started: fastANI
[2024-01-25 19:49:18,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg634222aa-004d-47d8-9a39-a11a6b0ccb83/GCF_014837235.1_ASM1483723v1_genomic.fna.gz --refList GCF_014837235.1_ASM1483723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837235.1_ASM1483723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:49:32,010] [INFO] Task succeeded: fastANI
[2024-01-25 19:49:32,020] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:49:32,021] [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_014837235.1	s__Limnohabitans_A sp014837235	100.0	1104	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903822825.1	s__Limnohabitans_A sp903822825	85.9799	701	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.95	99.93	0.93	0.91	3	-
GCF_003063335.1	s__Limnohabitans_A sp003063335	84.0818	671	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.88	99.88	0.96	0.96	2	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	83.9641	680	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.02	95.55	0.82	0.79	4	-
GCF_003063455.1	s__Limnohabitans_A parvus	83.9491	649	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063575.1	s__Limnohabitans_A sp003063575	83.9126	684	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063315.1	s__Limnohabitans_A sp003063315	83.9035	633	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	83.831	605	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063505.1	s__Limnohabitans_A sp003063505	83.7852	660	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	83.4666	632	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCF_001269385.1	s__Limnohabitans_A sp001269385	83.4023	673	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778285.1	s__Limnohabitans_A sp002778285	83.2814	637	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002778275.1	s__Limnohabitans_A sp002778275	83.0554	631	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269345.1	s__Limnohabitans_A sp001269345	82.9957	623	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063355.1	s__Limnohabitans_A sp003063355	82.857	627	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	82.0483	591	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421705.1	s__Xylophilus sp001421705	78.7741	388	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:49:32,023] [INFO] GTDB search result was written to GCF_014837235.1_ASM1483723v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:49:32,024] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:49:32,028] [INFO] DFAST_QC result json was written to GCF_014837235.1_ASM1483723v1_genomic.fna/dqc_result.json
[2024-01-25 19:49:32,029] [INFO] DFAST_QC completed!
[2024-01-25 19:49:32,029] [INFO] Total running time: 0h2m27s