[2024-01-24 15:06:36,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference
[2024-01-24 15:06:38,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,362] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,362] [INFO] Running command: gunzip -c /var/lib/cwl/stgbed5bc31-ab03-4348-aa77-3b472328db5e/GCF_900496965.1_LMG_3411T_genomic.fna.gz | prodigal -d GCF_900496965.1_LMG_3411T_genomic.fna/cds.fna -a GCF_900496965.1_LMG_3411T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:58,368] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:58,369] [INFO] Task started: HMMsearch
[2024-01-24 15:06:58,369] [INFO] Running command: hmmsearch --tblout GCF_900496965.1_LMG_3411T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/reference_markers.hmm GCF_900496965.1_LMG_3411T_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:58,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:58,764] [INFO] Found 6/6 markers.
[2024-01-24 15:06:58,832] [INFO] Query marker FASTA was written to GCF_900496965.1_LMG_3411T_genomic.fna/markers.fasta
[2024-01-24 15:06:58,833] [INFO] Task started: Blastn
[2024-01-24 15:06:58,833] [INFO] Running command: blastn -query GCF_900496965.1_LMG_3411T_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/reference_markers.fasta -out GCF_900496965.1_LMG_3411T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:59,976] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:59,983] [INFO] Selected 12 target genomes.
[2024-01-24 15:06:59,984] [INFO] Target genome list was writen to GCF_900496965.1_LMG_3411T_genomic.fna/target_genomes.txt
[2024-01-24 15:06:59,992] [INFO] Task started: fastANI
[2024-01-24 15:06:59,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed5bc31-ab03-4348-aa77-3b472328db5e/GCF_900496965.1_LMG_3411T_genomic.fna.gz --refList GCF_900496965.1_LMG_3411T_genomic.fna/target_genomes.txt --output GCF_900496965.1_LMG_3411T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:19,190] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:19,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:19,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:19,204] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:19,204] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:19,205] [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
Achromobacter agilis	strain=LMG 3411	GCA_900496965.1	1353888	1353888	type	True	100.0	2095	2100	95	conclusive
Achromobacter veterisilvae	strain=LMG 30378	GCA_900496975.1	2069367	2069367	type	True	90.9653	1659	2100	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	90.4164	1696	2100	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	90.4088	1703	2100	95	below_threshold
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	90.3954	1708	2100	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	90.3925	1748	2100	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	86.7028	1603	2100	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	86.0355	1405	2100	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	85.8433	1448	2100	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	82.0963	906	2100	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.4801	484	2100	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	77.1954	425	2100	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:19,206] [INFO] DFAST Taxonomy check result was written to GCF_900496965.1_LMG_3411T_genomic.fna/tc_result.tsv
[2024-01-24 15:07:19,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:19,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:19,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/checkm_data
[2024-01-24 15:07:19,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:19,267] [INFO] Task started: CheckM
[2024-01-24 15:07:19,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900496965.1_LMG_3411T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900496965.1_LMG_3411T_genomic.fna/checkm_input GCF_900496965.1_LMG_3411T_genomic.fna/checkm_result
[2024-01-24 15:08:14,520] [INFO] Task succeeded: CheckM
[2024-01-24 15:08:14,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:08:14,548] [INFO] ===== Completeness check finished =====
[2024-01-24 15:08:14,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:08:14,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900496965.1_LMG_3411T_genomic.fna/markers.fasta)
[2024-01-24 15:08:14,549] [INFO] Task started: Blastn
[2024-01-24 15:08:14,549] [INFO] Running command: blastn -query GCF_900496965.1_LMG_3411T_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ae3a562-552d-46d5-8d82-5c9475fe1c77/dqc_reference/reference_markers_gtdb.fasta -out GCF_900496965.1_LMG_3411T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:08:16,808] [INFO] Task succeeded: Blastn
[2024-01-24 15:08:16,814] [INFO] Selected 8 target genomes.
[2024-01-24 15:08:16,814] [INFO] Target genome list was writen to GCF_900496965.1_LMG_3411T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:08:16,826] [INFO] Task started: fastANI
[2024-01-24 15:08:16,827] [INFO] Running command: fastANI --query /var/lib/cwl/stgbed5bc31-ab03-4348-aa77-3b472328db5e/GCF_900496965.1_LMG_3411T_genomic.fna.gz --refList GCF_900496965.1_LMG_3411T_genomic.fna/target_genomes_gtdb.txt --output GCF_900496965.1_LMG_3411T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:32,552] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:32,567] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:32,567] [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_900496965.1	s__Achromobacter agilis	100.0	2095	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000757485.1	s__Achromobacter sp000757485	91.8546	1869	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900496975.1	s__Achromobacter veterisilvae	90.9752	1658	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571365.1	s__Achromobacter denitrificans	90.4088	1703	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
GCF_002885955.2	s__Achromobacter pulmonis_A	88.5075	1535	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_902859735.1	s__Achromobacter aegrifaciens	87.6435	1603	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.14	98.95	0.96	0.93	10	-
GCF_902859645.1	s__Achromobacter insuavis	86.0576	1403	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_016127315.1	s__Achromobacter insuavis_A	85.9111	1446	2100	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:32,569] [INFO] GTDB search result was written to GCF_900496965.1_LMG_3411T_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:32,570] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:32,573] [INFO] DFAST_QC result json was written to GCF_900496965.1_LMG_3411T_genomic.fna/dqc_result.json
[2024-01-24 15:08:32,574] [INFO] DFAST_QC completed!
[2024-01-24 15:08:32,574] [INFO] Total running time: 0h1m56s