[2024-01-24 13:31:44,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference
[2024-01-24 13:31:45,573] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,574] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,574] [INFO] Running command: gunzip -c /var/lib/cwl/stgd04dc86a-190d-4607-8f42-e6af2796ff77/GCF_004217045.1_ASM421704v1_genomic.fna.gz | prodigal -d GCF_004217045.1_ASM421704v1_genomic.fna/cds.fna -a GCF_004217045.1_ASM421704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:05,280] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:05,281] [INFO] Task started: HMMsearch
[2024-01-24 13:32:05,281] [INFO] Running command: hmmsearch --tblout GCF_004217045.1_ASM421704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/reference_markers.hmm GCF_004217045.1_ASM421704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,622] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,676] [INFO] Query marker FASTA was written to GCF_004217045.1_ASM421704v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,676] [INFO] Task started: Blastn
[2024-01-24 13:32:05,676] [INFO] Running command: blastn -query GCF_004217045.1_ASM421704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/reference_markers.fasta -out GCF_004217045.1_ASM421704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,808] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,811] [INFO] Selected 15 target genomes.
[2024-01-24 13:32:06,812] [INFO] Target genome list was writen to GCF_004217045.1_ASM421704v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,817] [INFO] Task started: fastANI
[2024-01-24 13:32:06,817] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04dc86a-190d-4607-8f42-e6af2796ff77/GCF_004217045.1_ASM421704v1_genomic.fna.gz --refList GCF_004217045.1_ASM421704v1_genomic.fna/target_genomes.txt --output GCF_004217045.1_ASM421704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:28,436] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:28,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:28,437] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:28,450] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:28,450] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:28,450] [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
Cupriavidus agavae	strain=ASC-9842	GCA_004217045.1	1001822	1001822	type	True	100.0	1919	1920	95	conclusive
Cupriavidus campinensis	strain=LMG 19282	GCA_905397395.1	151783	151783	type	True	85.5309	1309	1920	95	below_threshold
Cupriavidus pauculus	strain=FDAARGOS_1472	GCA_019931045.1	82633	82633	type	True	84.6966	1314	1920	95	below_threshold
Cupriavidus pauculus	strain=CCUG 12507	GCA_008801835.1	82633	82633	type	True	84.64	1295	1920	95	below_threshold
Cupriavidus metallidurans	strain=CH34	GCA_000196015.1	119219	119219	type	True	84.1661	1180	1920	95	below_threshold
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	83.9236	1165	1920	95	below_threshold
Cupriavidus alkaliphilus	strain=ASC-732	GCA_900094595.1	942866	942866	type	True	83.8938	1166	1920	95	below_threshold
Cupriavidus oxalaticus	strain=Ox1	GCA_016894385.1	96344	96344	type	True	83.7048	1162	1920	95	below_threshold
Cupriavidus taiwanensis	strain=LMG 19424	GCA_000069785.1	164546	164546	suspected-type	True	83.6348	1184	1920	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	82.8573	1128	1920	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	82.668	1042	1920	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	78.4185	620	1920	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.308	494	1920	95	below_threshold
Massilia agilis	strain=JCM 31605	GCA_024756255.1	1811226	1811226	type	True	78.2847	502	1920	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	77.9828	489	1920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:28,452] [INFO] DFAST Taxonomy check result was written to GCF_004217045.1_ASM421704v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:28,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:28,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:28,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/checkm_data
[2024-01-24 13:32:28,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:28,512] [INFO] Task started: CheckM
[2024-01-24 13:32:28,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217045.1_ASM421704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217045.1_ASM421704v1_genomic.fna/checkm_input GCF_004217045.1_ASM421704v1_genomic.fna/checkm_result
[2024-01-24 13:33:33,561] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:33,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,600] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:33,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:33,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217045.1_ASM421704v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:33,601] [INFO] Task started: Blastn
[2024-01-24 13:33:33,602] [INFO] Running command: blastn -query GCF_004217045.1_ASM421704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f5802eb-a1af-4440-a1a9-d9fd09cb28a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217045.1_ASM421704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:36,038] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:36,049] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:36,050] [INFO] Target genome list was writen to GCF_004217045.1_ASM421704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:36,072] [INFO] Task started: fastANI
[2024-01-24 13:33:36,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04dc86a-190d-4607-8f42-e6af2796ff77/GCF_004217045.1_ASM421704v1_genomic.fna.gz --refList GCF_004217045.1_ASM421704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217045.1_ASM421704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:52,798] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:52,807] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:52,807] [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_004217045.1	s__Cupriavidus sp004217045	100.0	1919	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003854935.1	s__Cupriavidus pauculus_C	87.4469	1470	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503625.1	s__Cupriavidus sp005503625	87.1329	1500	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	98.70	98.70	0.91	0.91	2	-
GCF_018729255.1	s__Cupriavidus sp018729255	86.6067	1420	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104095.1	s__Cupriavidus sp900104095	86.2871	1396	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663685.1	s__Cupriavidus necator_C	86.2617	1400	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002858765.1	s__Cupriavidus pauculus_B	86.1621	1418	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652915.1	s__Cupriavidus sp001652915	86.1453	1425	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_905397395.1	s__Cupriavidus campinensis	85.5378	1308	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	97.28	95.05	0.89	0.86	6	-
GCF_017814975.1	s__Cupriavidus sp017814975	83.299	1181	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:52,809] [INFO] GTDB search result was written to GCF_004217045.1_ASM421704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:52,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:52,813] [INFO] DFAST_QC result json was written to GCF_004217045.1_ASM421704v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:52,813] [INFO] DFAST_QC completed!
[2024-01-24 13:33:52,813] [INFO] Total running time: 0h2m9s