[2024-01-24 13:17:34,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,677] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference
[2024-01-24 13:17:36,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,152] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg372e5e3f-a9b7-45a4-9027-036ab4ef77c0/GCF_003034845.1_ASM303484v1_genomic.fna.gz | prodigal -d GCF_003034845.1_ASM303484v1_genomic.fna/cds.fna -a GCF_003034845.1_ASM303484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:48,347] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:48,348] [INFO] Task started: HMMsearch
[2024-01-24 13:17:48,348] [INFO] Running command: hmmsearch --tblout GCF_003034845.1_ASM303484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/reference_markers.hmm GCF_003034845.1_ASM303484v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:48,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:48,630] [INFO] Found 6/6 markers.
[2024-01-24 13:17:48,662] [INFO] Query marker FASTA was written to GCF_003034845.1_ASM303484v1_genomic.fna/markers.fasta
[2024-01-24 13:17:48,662] [INFO] Task started: Blastn
[2024-01-24 13:17:48,662] [INFO] Running command: blastn -query GCF_003034845.1_ASM303484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/reference_markers.fasta -out GCF_003034845.1_ASM303484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:49,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:49,769] [INFO] Selected 20 target genomes.
[2024-01-24 13:17:49,769] [INFO] Target genome list was writen to GCF_003034845.1_ASM303484v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:49,776] [INFO] Task started: fastANI
[2024-01-24 13:17:49,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg372e5e3f-a9b7-45a4-9027-036ab4ef77c0/GCF_003034845.1_ASM303484v1_genomic.fna.gz --refList GCF_003034845.1_ASM303484v1_genomic.fna/target_genomes.txt --output GCF_003034845.1_ASM303484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:09,533] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:09,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:09,534] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:09,550] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:09,550] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:09,550] [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
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	84.0522	755	1200	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	83.8814	758	1200	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	82.4684	567	1200	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	82.0998	579	1200	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	81.6381	596	1200	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	81.4449	601	1200	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	81.424	570	1200	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	81.1357	548	1200	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	81.0688	573	1200	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	80.8981	608	1200	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	80.8936	634	1200	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	80.8341	646	1200	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	80.7404	555	1200	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.6585	556	1200	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	80.5553	539	1200	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	80.1351	474	1200	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.0139	524	1200	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.7173	496	1200	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.4908	467	1200	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.6495	357	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,552] [INFO] DFAST Taxonomy check result was written to GCF_003034845.1_ASM303484v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:09,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:09,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:09,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/checkm_data
[2024-01-24 13:18:09,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:09,594] [INFO] Task started: CheckM
[2024-01-24 13:18:09,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003034845.1_ASM303484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003034845.1_ASM303484v1_genomic.fna/checkm_input GCF_003034845.1_ASM303484v1_genomic.fna/checkm_result
[2024-01-24 13:18:51,756] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:51,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:51,776] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:51,777] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:51,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003034845.1_ASM303484v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:51,778] [INFO] Task started: Blastn
[2024-01-24 13:18:51,778] [INFO] Running command: blastn -query GCF_003034845.1_ASM303484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf797b16-07a2-4f7a-8fa4-676703cca417/dqc_reference/reference_markers_gtdb.fasta -out GCF_003034845.1_ASM303484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:53,914] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:53,924] [INFO] Selected 14 target genomes.
[2024-01-24 13:18:53,924] [INFO] Target genome list was writen to GCF_003034845.1_ASM303484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:53,942] [INFO] Task started: fastANI
[2024-01-24 13:18:53,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg372e5e3f-a9b7-45a4-9027-036ab4ef77c0/GCF_003034845.1_ASM303484v1_genomic.fna.gz --refList GCF_003034845.1_ASM303484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003034845.1_ASM303484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:07,583] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:07,598] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:07,599] [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_003034845.1	s__Thauera_A sp003034845	100.0	1199	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014489115.1	s__Thauera_A sp014489115	85.4963	857	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004801305.1	s__Thauera_A rhizosphaerae	84.0556	755	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801295.1	s__Thauera_A nasutitermitis	83.8332	763	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	82.4465	568	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	82.3512	585	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	81.6134	599	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	81.4321	569	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_006496635.1	s__Azoarcus sp006496635	81.2107	652	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911025.1	s__Azoarcus sp012911025	81.1033	615	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345255.1	s__Thauera_A hydrothermalis	80.8876	609	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	98.04	97.85	0.92	0.92	3	-
GCF_004361735.1	s__Azoarcus indigens	80.8364	646	1200	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900156155.1	s__Aromatoleum tolulyticum	80.7297	555	1200	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	80.6653	537	1200	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 13:19:07,601] [INFO] GTDB search result was written to GCF_003034845.1_ASM303484v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:07,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:07,606] [INFO] DFAST_QC result json was written to GCF_003034845.1_ASM303484v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:07,607] [INFO] DFAST_QC completed!
[2024-01-24 13:19:07,607] [INFO] Total running time: 0h1m33s