[2024-01-24 12:36:58,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference
[2024-01-24 12:36:59,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,954] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a318ff0-b851-4122-bbab-04bef5f6b0f3/GCF_014297445.1_ASM1429744v1_genomic.fna.gz | prodigal -d GCF_014297445.1_ASM1429744v1_genomic.fna/cds.fna -a GCF_014297445.1_ASM1429744v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:22,556] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:22,557] [INFO] Task started: HMMsearch
[2024-01-24 12:37:22,557] [INFO] Running command: hmmsearch --tblout GCF_014297445.1_ASM1429744v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/reference_markers.hmm GCF_014297445.1_ASM1429744v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:22,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:22,964] [INFO] Found 6/6 markers.
[2024-01-24 12:37:23,022] [INFO] Query marker FASTA was written to GCF_014297445.1_ASM1429744v1_genomic.fna/markers.fasta
[2024-01-24 12:37:23,022] [INFO] Task started: Blastn
[2024-01-24 12:37:23,022] [INFO] Running command: blastn -query GCF_014297445.1_ASM1429744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/reference_markers.fasta -out GCF_014297445.1_ASM1429744v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:24,022] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:24,025] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:24,026] [INFO] Target genome list was writen to GCF_014297445.1_ASM1429744v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:24,029] [INFO] Task started: fastANI
[2024-01-24 12:37:24,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a318ff0-b851-4122-bbab-04bef5f6b0f3/GCF_014297445.1_ASM1429744v1_genomic.fna.gz --refList GCF_014297445.1_ASM1429744v1_genomic.fna/target_genomes.txt --output GCF_014297445.1_ASM1429744v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:39,903] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:39,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:39,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:39,914] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:39,915] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:39,915] [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
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.5187	906	2032	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	82.3735	1011	2032	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	82.3139	870	2032	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	82.1655	879	2032	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	82.1033	987	2032	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	82.0027	1051	2032	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.9236	833	2032	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.7871	755	2032	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	81.5647	930	2032	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.0748	881	2032	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.9783	767	2032	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.3094	725	2032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:39,916] [INFO] DFAST Taxonomy check result was written to GCF_014297445.1_ASM1429744v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:39,917] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:39,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:39,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/checkm_data
[2024-01-24 12:37:39,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:39,980] [INFO] Task started: CheckM
[2024-01-24 12:37:39,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297445.1_ASM1429744v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297445.1_ASM1429744v1_genomic.fna/checkm_input GCF_014297445.1_ASM1429744v1_genomic.fna/checkm_result
[2024-01-24 12:39:12,265] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:12,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:12,290] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:12,290] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:12,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297445.1_ASM1429744v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:12,291] [INFO] Task started: Blastn
[2024-01-24 12:39:12,291] [INFO] Running command: blastn -query GCF_014297445.1_ASM1429744v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27587a19-68af-440d-81cc-92ff9d219156/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297445.1_ASM1429744v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:14,171] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:14,175] [INFO] Selected 18 target genomes.
[2024-01-24 12:39:14,176] [INFO] Target genome list was writen to GCF_014297445.1_ASM1429744v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:14,207] [INFO] Task started: fastANI
[2024-01-24 12:39:14,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a318ff0-b851-4122-bbab-04bef5f6b0f3/GCF_014297445.1_ASM1429744v1_genomic.fna.gz --refList GCF_014297445.1_ASM1429744v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297445.1_ASM1429744v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:36,622] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:36,643] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:36,643] [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_014297445.1	s__Ramlibacter sp014297445	100.0	2030	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013087525.1	s__Ramlibacter sp013087525	82.8653	1037	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144865.1	s__Ramlibacter sp004144865	82.8262	836	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213325.1	s__Ramlibacter sp016213325	82.8153	1071	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297465.1	s__Ramlibacter sp014297465	82.7228	1022	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681975.1	s__Ramlibacter sp004681975	82.5484	903	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013697775.1	s__Ramlibacter sp013697775	82.4901	789	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	82.4621	917	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	82.3854	1010	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	82.3698	918	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016641735.1	s__Ramlibacter sp016641735	82.2996	870	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016654015.1	s__Ramlibacter ginsenosidimutans	82.2183	913	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004682015.1	s__Ramlibacter henchirensis	82.1729	878	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722765.1	s__Ramlibacter alkalitolerans	82.1142	985	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927085.1	s__Ramlibacter sp012927085	81.9956	1051	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	81.9263	833	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833165.1	s__Ramlibacter sp007833165	81.7819	1005	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	81.0522	884	2032	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:36,646] [INFO] GTDB search result was written to GCF_014297445.1_ASM1429744v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:36,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:36,653] [INFO] DFAST_QC result json was written to GCF_014297445.1_ASM1429744v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:36,654] [INFO] DFAST_QC completed!
[2024-01-24 12:39:36,654] [INFO] Total running time: 0h2m38s