[2024-01-25 17:45:35,565] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:35,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:35,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference
[2024-01-25 17:45:36,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:36,706] [INFO] Task started: Prodigal
[2024-01-25 17:45:36,707] [INFO] Running command: gunzip -c /var/lib/cwl/stgf65f9407-bca0-40f2-9e4b-3a643467a312/GCF_000310225.1_ASM31022v1_genomic.fna.gz | prodigal -d GCF_000310225.1_ASM31022v1_genomic.fna/cds.fna -a GCF_000310225.1_ASM31022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:49,093] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:49,094] [INFO] Task started: HMMsearch
[2024-01-25 17:45:49,094] [INFO] Running command: hmmsearch --tblout GCF_000310225.1_ASM31022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/reference_markers.hmm GCF_000310225.1_ASM31022v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:49,380] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:49,381] [INFO] Found 6/6 markers.
[2024-01-25 17:45:49,422] [INFO] Query marker FASTA was written to GCF_000310225.1_ASM31022v1_genomic.fna/markers.fasta
[2024-01-25 17:45:49,422] [INFO] Task started: Blastn
[2024-01-25 17:45:49,422] [INFO] Running command: blastn -query GCF_000310225.1_ASM31022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/reference_markers.fasta -out GCF_000310225.1_ASM31022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:50,512] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:50,515] [INFO] Selected 14 target genomes.
[2024-01-25 17:45:50,515] [INFO] Target genome list was writen to GCF_000310225.1_ASM31022v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:50,526] [INFO] Task started: fastANI
[2024-01-25 17:45:50,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgf65f9407-bca0-40f2-9e4b-3a643467a312/GCF_000310225.1_ASM31022v1_genomic.fna.gz --refList GCF_000310225.1_ASM31022v1_genomic.fna/target_genomes.txt --output GCF_000310225.1_ASM31022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:03,936] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:03,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:03,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:03,946] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:03,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:03,946] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	100.0	1383	1397	95	conclusive
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	91.8814	913	1397	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	85.1702	707	1397	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	85.0703	712	1397	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	84.7687	740	1397	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	84.7038	690	1397	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	84.2076	683	1397	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	83.543	664	1397	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	83.5339	654	1397	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	81.1264	620	1397	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.4054	541	1397	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	80.048	516	1397	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.0215	492	1397	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.6187	337	1397	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:03,947] [INFO] DFAST Taxonomy check result was written to GCF_000310225.1_ASM31022v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:03,948] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:03,948] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:03,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/checkm_data
[2024-01-25 17:46:03,949] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:03,997] [INFO] Task started: CheckM
[2024-01-25 17:46:03,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000310225.1_ASM31022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000310225.1_ASM31022v1_genomic.fna/checkm_input GCF_000310225.1_ASM31022v1_genomic.fna/checkm_result
[2024-01-25 17:46:43,030] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:43,031] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:43,049] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:43,050] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:43,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000310225.1_ASM31022v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:43,050] [INFO] Task started: Blastn
[2024-01-25 17:46:43,050] [INFO] Running command: blastn -query GCF_000310225.1_ASM31022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0764b6f0-f126-49f7-87d6-fa4e391a8bbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_000310225.1_ASM31022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:45,364] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:45,366] [INFO] Selected 9 target genomes.
[2024-01-25 17:46:45,366] [INFO] Target genome list was writen to GCF_000310225.1_ASM31022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:45,377] [INFO] Task started: fastANI
[2024-01-25 17:46:45,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgf65f9407-bca0-40f2-9e4b-3a643467a312/GCF_000310225.1_ASM31022v1_genomic.fna.gz --refList GCF_000310225.1_ASM31022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000310225.1_ASM31022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:46:54,376] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:54,383] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:46:54,383] [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_000310225.1	s__Thauera phenylacetica	100.0	1382	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003963015.1	s__Thauera sp003963015	94.0694	917	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	92.4157	624	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	91.8811	912	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	88.4806	561	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	87.2818	724	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	86.7994	568	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_001591165.1	s__Thauera butanivorans	84.1723	686	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	83.7374	731	1397	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:46:54,385] [INFO] GTDB search result was written to GCF_000310225.1_ASM31022v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:46:54,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:46:54,388] [INFO] DFAST_QC result json was written to GCF_000310225.1_ASM31022v1_genomic.fna/dqc_result.json
[2024-01-25 17:46:54,388] [INFO] DFAST_QC completed!
[2024-01-25 17:46:54,388] [INFO] Total running time: 0h1m19s