[2024-01-24 14:21:50,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,620] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference
[2024-01-24 14:21:52,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,035] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgfbad1780-c8dc-4fd7-85ba-e0ff0285a30b/GCF_017894365.1_ASM1789436v1_genomic.fna.gz | prodigal -d GCF_017894365.1_ASM1789436v1_genomic.fna/cds.fna -a GCF_017894365.1_ASM1789436v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:06,183] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:06,183] [INFO] Task started: HMMsearch
[2024-01-24 14:22:06,183] [INFO] Running command: hmmsearch --tblout GCF_017894365.1_ASM1789436v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/reference_markers.hmm GCF_017894365.1_ASM1789436v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:06,532] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:06,533] [INFO] Found 6/6 markers.
[2024-01-24 14:22:06,571] [INFO] Query marker FASTA was written to GCF_017894365.1_ASM1789436v1_genomic.fna/markers.fasta
[2024-01-24 14:22:06,572] [INFO] Task started: Blastn
[2024-01-24 14:22:06,572] [INFO] Running command: blastn -query GCF_017894365.1_ASM1789436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/reference_markers.fasta -out GCF_017894365.1_ASM1789436v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:07,655] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:07,658] [INFO] Selected 8 target genomes.
[2024-01-24 14:22:07,659] [INFO] Target genome list was writen to GCF_017894365.1_ASM1789436v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:07,663] [INFO] Task started: fastANI
[2024-01-24 14:22:07,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbad1780-c8dc-4fd7-85ba-e0ff0285a30b/GCF_017894365.1_ASM1789436v1_genomic.fna.gz --refList GCF_017894365.1_ASM1789436v1_genomic.fna/target_genomes.txt --output GCF_017894365.1_ASM1789436v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:17,703] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:17,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:17,704] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:17,712] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:17,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:17,713] [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
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	100.0	1455	1458	95	conclusive
Aromatoleum bremense	strain=PbN1	GCA_012910925.1	76115	76115	type	True	99.9203	1344	1458	95	conclusive
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	94.6929	1091	1458	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	92.4448	1051	1458	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	92.1466	1011	1458	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	82.4198	804	1458	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.7145	392	1458	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.0833	267	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:17,714] [INFO] DFAST Taxonomy check result was written to GCF_017894365.1_ASM1789436v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:17,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:17,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:17,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/checkm_data
[2024-01-24 14:22:17,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:17,759] [INFO] Task started: CheckM
[2024-01-24 14:22:17,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017894365.1_ASM1789436v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017894365.1_ASM1789436v1_genomic.fna/checkm_input GCF_017894365.1_ASM1789436v1_genomic.fna/checkm_result
[2024-01-24 14:23:02,749] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:02,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:02,772] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:02,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:02,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017894365.1_ASM1789436v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:02,773] [INFO] Task started: Blastn
[2024-01-24 14:23:02,773] [INFO] Running command: blastn -query GCF_017894365.1_ASM1789436v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0cd662a-f54a-4af7-9967-0a3ef9ec6af9/dqc_reference/reference_markers_gtdb.fasta -out GCF_017894365.1_ASM1789436v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:04,782] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:04,787] [INFO] Selected 5 target genomes.
[2024-01-24 14:23:04,787] [INFO] Target genome list was writen to GCF_017894365.1_ASM1789436v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:04,796] [INFO] Task started: fastANI
[2024-01-24 14:23:04,796] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbad1780-c8dc-4fd7-85ba-e0ff0285a30b/GCF_017894365.1_ASM1789436v1_genomic.fna.gz --refList GCF_017894365.1_ASM1789436v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017894365.1_ASM1789436v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:10,798] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,804] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:10,804] [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_017894365.1	s__Aromatoleum bremense	100.0	1455	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_012910705.1	s__Aromatoleum anaerobium	94.7048	1047	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025965.1	s__Aromatoleum aromaticum	92.44	1053	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCF_012910785.1	s__Aromatoleum buckelii	92.2625	991	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	91.7973	1008	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,806] [INFO] GTDB search result was written to GCF_017894365.1_ASM1789436v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:10,806] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:10,809] [INFO] DFAST_QC result json was written to GCF_017894365.1_ASM1789436v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:10,809] [INFO] DFAST_QC completed!
[2024-01-24 14:23:10,810] [INFO] Total running time: 0h1m20s