[2024-01-24 15:19:04,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference
[2024-01-24 15:19:06,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:06,120] [INFO] Task started: Prodigal
[2024-01-24 15:19:06,120] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8294191-d8e6-493c-a095-2928857a526d/GCF_003063455.1_ASM306345v1_genomic.fna.gz | prodigal -d GCF_003063455.1_ASM306345v1_genomic.fna/cds.fna -a GCF_003063455.1_ASM306345v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:18,941] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:18,941] [INFO] Task started: HMMsearch
[2024-01-24 15:19:18,942] [INFO] Running command: hmmsearch --tblout GCF_003063455.1_ASM306345v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/reference_markers.hmm GCF_003063455.1_ASM306345v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:19,204] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:19,206] [INFO] Found 6/6 markers.
[2024-01-24 15:19:19,234] [INFO] Query marker FASTA was written to GCF_003063455.1_ASM306345v1_genomic.fna/markers.fasta
[2024-01-24 15:19:19,234] [INFO] Task started: Blastn
[2024-01-24 15:19:19,234] [INFO] Running command: blastn -query GCF_003063455.1_ASM306345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/reference_markers.fasta -out GCF_003063455.1_ASM306345v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:20,124] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:20,127] [INFO] Selected 19 target genomes.
[2024-01-24 15:19:20,128] [INFO] Target genome list was writen to GCF_003063455.1_ASM306345v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:20,138] [INFO] Task started: fastANI
[2024-01-24 15:19:20,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8294191-d8e6-493c-a095-2928857a526d/GCF_003063455.1_ASM306345v1_genomic.fna.gz --refList GCF_003063455.1_ASM306345v1_genomic.fna/target_genomes.txt --output GCF_003063455.1_ASM306345v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:35,899] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:35,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:35,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:35,921] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:35,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:35,921] [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 parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	100.0	983	986	95	conclusive
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	84.8914	688	986	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	83.8566	655	986	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	79.5488	356	986	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	79.1708	409	986	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	79.0965	399	986	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.0168	355	986	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	78.9691	436	986	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	78.8669	418	986	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	78.766	316	986	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.7132	377	986	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.6814	391	986	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	78.6323	310	986	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	78.4531	327	986	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	78.2073	363	986	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.1569	337	986	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.9728	309	986	95	below_threshold
Brachymonas chironomi	strain=DSM 19884	GCA_000374625.1	491919	491919	type	True	77.8799	229	986	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.8413	343	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:35,923] [INFO] DFAST Taxonomy check result was written to GCF_003063455.1_ASM306345v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:35,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:35,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:35,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/checkm_data
[2024-01-24 15:19:35,925] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:35,956] [INFO] Task started: CheckM
[2024-01-24 15:19:35,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003063455.1_ASM306345v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003063455.1_ASM306345v1_genomic.fna/checkm_input GCF_003063455.1_ASM306345v1_genomic.fna/checkm_result
[2024-01-24 15:20:28,691] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:28,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:28,708] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:28,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:28,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003063455.1_ASM306345v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:28,710] [INFO] Task started: Blastn
[2024-01-24 15:20:28,710] [INFO] Running command: blastn -query GCF_003063455.1_ASM306345v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf150792f-526f-4abf-beb6-1d36f4b81ac5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003063455.1_ASM306345v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:30,450] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:30,455] [INFO] Selected 14 target genomes.
[2024-01-24 15:20:30,455] [INFO] Target genome list was writen to GCF_003063455.1_ASM306345v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:30,469] [INFO] Task started: fastANI
[2024-01-24 15:20:30,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8294191-d8e6-493c-a095-2928857a526d/GCF_003063455.1_ASM306345v1_genomic.fna.gz --refList GCF_003063455.1_ASM306345v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003063455.1_ASM306345v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:41,745] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:41,758] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:41,758] [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_003063455.1	s__Limnohabitans_A parvus	100.0	985	986	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_017986605.1	s__Limnohabitans_A sp017986605	90.2125	545	986	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	88.3944	774	986	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_003063435.1	s__Limnohabitans_A sp003063435	86.9087	685	986	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_001517545.1	s__Limnohabitans_A sp001517545	86.2184	731	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	96.89	95.29	0.97	0.96	4	-
GCF_003063665.1	s__Limnohabitans_A sp003063665	85.9923	724	986	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_002778275.1	s__Limnohabitans_A sp002778275	85.7696	736	986	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	85.4541	709	986	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	85.4364	676	986	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_001412535.1	s__Limnohabitans_A sp001412535	85.2882	680	986	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	85.2442	695	986	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_001269385.1	s__Limnohabitans_A sp001269385	85.107	699	986	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	84.7228	705	986	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	84.5354	644	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:41,760] [INFO] GTDB search result was written to GCF_003063455.1_ASM306345v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:41,761] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:41,765] [INFO] DFAST_QC result json was written to GCF_003063455.1_ASM306345v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:41,766] [INFO] DFAST_QC completed!
[2024-01-24 15:20:41,766] [INFO] Total running time: 0h1m37s