[2024-01-24 13:55:48,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:48,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:48,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference
[2024-01-24 13:55:49,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:49,690] [INFO] Task started: Prodigal
[2024-01-24 13:55:49,690] [INFO] Running command: gunzip -c /var/lib/cwl/stg55df45d1-84b7-49a1-9da4-1239d2de2dc3/GCF_012910955.1_ASM1291095v1_genomic.fna.gz | prodigal -d GCF_012910955.1_ASM1291095v1_genomic.fna/cds.fna -a GCF_012910955.1_ASM1291095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:05,592] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:05,593] [INFO] Task started: HMMsearch
[2024-01-24 13:56:05,593] [INFO] Running command: hmmsearch --tblout GCF_012910955.1_ASM1291095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/reference_markers.hmm GCF_012910955.1_ASM1291095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:05,914] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:05,916] [INFO] Found 6/6 markers.
[2024-01-24 13:56:05,966] [INFO] Query marker FASTA was written to GCF_012910955.1_ASM1291095v1_genomic.fna/markers.fasta
[2024-01-24 13:56:05,966] [INFO] Task started: Blastn
[2024-01-24 13:56:05,967] [INFO] Running command: blastn -query GCF_012910955.1_ASM1291095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/reference_markers.fasta -out GCF_012910955.1_ASM1291095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:06,942] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:06,945] [INFO] Selected 13 target genomes.
[2024-01-24 13:56:06,946] [INFO] Target genome list was writen to GCF_012910955.1_ASM1291095v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:06,955] [INFO] Task started: fastANI
[2024-01-24 13:56:06,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg55df45d1-84b7-49a1-9da4-1239d2de2dc3/GCF_012910955.1_ASM1291095v1_genomic.fna.gz --refList GCF_012910955.1_ASM1291095v1_genomic.fna/target_genomes.txt --output GCF_012910955.1_ASM1291095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:20,775] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:20,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:20,777] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:20,792] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:20,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:20,793] [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 diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	100.0	1656	1660	95	conclusive
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	84.2914	1132	1660	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	83.7227	1049	1660	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	83.4834	896	1660	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	83.2046	1008	1660	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	83.1704	1022	1660	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	82.009	763	1660	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	81.9881	784	1660	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	81.6687	695	1660	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	81.5158	677	1660	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	80.2537	569	1660	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.7662	411	1660	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.4328	332	1660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:20,794] [INFO] DFAST Taxonomy check result was written to GCF_012910955.1_ASM1291095v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:20,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:20,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:20,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/checkm_data
[2024-01-24 13:56:20,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:20,845] [INFO] Task started: CheckM
[2024-01-24 13:56:20,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012910955.1_ASM1291095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012910955.1_ASM1291095v1_genomic.fna/checkm_input GCF_012910955.1_ASM1291095v1_genomic.fna/checkm_result
[2024-01-24 13:57:07,918] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:07,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:07,943] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:07,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:07,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012910955.1_ASM1291095v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:07,945] [INFO] Task started: Blastn
[2024-01-24 13:57:07,945] [INFO] Running command: blastn -query GCF_012910955.1_ASM1291095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg642e290d-fec1-4306-b424-245898d56eee/dqc_reference/reference_markers_gtdb.fasta -out GCF_012910955.1_ASM1291095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:09,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:09,787] [INFO] Selected 15 target genomes.
[2024-01-24 13:57:09,787] [INFO] Target genome list was writen to GCF_012910955.1_ASM1291095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:09,822] [INFO] Task started: fastANI
[2024-01-24 13:57:09,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg55df45d1-84b7-49a1-9da4-1239d2de2dc3/GCF_012910955.1_ASM1291095v1_genomic.fna.gz --refList GCF_012910955.1_ASM1291095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012910955.1_ASM1291095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:26,560] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:26,575] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:26,575] [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_012910955.1	s__Aromatoleum diolicum	100.0	1656	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012911005.1	s__Aromatoleum toluolicum	84.2834	1134	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156155.1	s__Aromatoleum tolulyticum	83.7303	1048	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001190925.1	s__Aromatoleum sp001190925	83.6467	1068	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014822185.1	s__Aromatoleum sp014822185	83.5682	1047	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910905.1	s__Aromatoleum toluvorans	83.4877	895	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	83.2021	1018	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910805.1	s__Aromatoleum evansii	83.1924	1009	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628555.1	s__Aromatoleum sp003628555	83.1435	939	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349945.1	s__Aromatoleum sp000349945	82.5031	961	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910785.1	s__Aromatoleum buckelii	81.6792	699	1660	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	81.6378	715	1660	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	81.4955	678	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	98.48	98.48	0.91	0.91	2	-
GCF_001591165.1	s__Thauera butanivorans	80.2401	570	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489115.1	s__Thauera_A sp014489115	79.9705	608	1660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:26,577] [INFO] GTDB search result was written to GCF_012910955.1_ASM1291095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:26,578] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:26,581] [INFO] DFAST_QC result json was written to GCF_012910955.1_ASM1291095v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:26,581] [INFO] DFAST_QC completed!
[2024-01-24 13:57:26,581] [INFO] Total running time: 0h1m38s