[2024-01-24 14:05:48,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference
[2024-01-24 14:05:49,517] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:49,518] [INFO] Task started: Prodigal
[2024-01-24 14:05:49,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg761fc352-1b07-4548-b0e5-1b112d4c29f3/GCF_001682385.1_ASM168238v1_genomic.fna.gz | prodigal -d GCF_001682385.1_ASM168238v1_genomic.fna/cds.fna -a GCF_001682385.1_ASM168238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:03,317] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:03,317] [INFO] Task started: HMMsearch
[2024-01-24 14:06:03,317] [INFO] Running command: hmmsearch --tblout GCF_001682385.1_ASM168238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/reference_markers.hmm GCF_001682385.1_ASM168238v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,653] [INFO] Found 6/6 markers.
[2024-01-24 14:06:03,706] [INFO] Query marker FASTA was written to GCF_001682385.1_ASM168238v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,708] [INFO] Task started: Blastn
[2024-01-24 14:06:03,708] [INFO] Running command: blastn -query GCF_001682385.1_ASM168238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/reference_markers.fasta -out GCF_001682385.1_ASM168238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:04,866] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:04,870] [INFO] Selected 19 target genomes.
[2024-01-24 14:06:04,870] [INFO] Target genome list was writen to GCF_001682385.1_ASM168238v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:04,884] [INFO] Task started: fastANI
[2024-01-24 14:06:04,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg761fc352-1b07-4548-b0e5-1b112d4c29f3/GCF_001682385.1_ASM168238v1_genomic.fna.gz --refList GCF_001682385.1_ASM168238v1_genomic.fna/target_genomes.txt --output GCF_001682385.1_ASM168238v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:24,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:24,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:24,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:24,324] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:24,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:24,325] [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 indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	82.5885	903	1483	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	82.5718	900	1483	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	82.2263	618	1483	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	81.8808	639	1483	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	81.8669	650	1483	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	81.8375	669	1483	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	81.6795	741	1483	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	81.5625	686	1483	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	81.5164	642	1483	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	81.4738	655	1483	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	81.4512	675	1483	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	81.1321	649	1483	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.6882	680	1483	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	80.62	693	1483	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.1041	594	1483	95	below_threshold
Aromatoleum diolicum	strain=22Lin	GCA_012910955.1	75796	75796	type	True	80.0916	602	1483	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.9812	567	1483	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.5901	567	1483	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.5116	399	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:24,327] [INFO] DFAST Taxonomy check result was written to GCF_001682385.1_ASM168238v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:24,327] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:24,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:24,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/checkm_data
[2024-01-24 14:06:24,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:24,373] [INFO] Task started: CheckM
[2024-01-24 14:06:24,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001682385.1_ASM168238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001682385.1_ASM168238v1_genomic.fna/checkm_input GCF_001682385.1_ASM168238v1_genomic.fna/checkm_result
[2024-01-24 14:07:18,595] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:18,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:18,617] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:18,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:18,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001682385.1_ASM168238v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:18,618] [INFO] Task started: Blastn
[2024-01-24 14:07:18,619] [INFO] Running command: blastn -query GCF_001682385.1_ASM168238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de0be28-7575-42e6-a6ed-890a00e24ae2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001682385.1_ASM168238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:20,826] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:20,830] [INFO] Selected 18 target genomes.
[2024-01-24 14:07:20,831] [INFO] Target genome list was writen to GCF_001682385.1_ASM168238v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:20,849] [INFO] Task started: fastANI
[2024-01-24 14:07:20,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg761fc352-1b07-4548-b0e5-1b112d4c29f3/GCF_001682385.1_ASM168238v1_genomic.fna.gz --refList GCF_001682385.1_ASM168238v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001682385.1_ASM168238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:38,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:38,747] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:38,748] [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_001682385.1	s__Azoarcus olearius	100.0	1482	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	conclusive
GCF_006496635.1	s__Azoarcus sp006496635	86.3478	1163	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361735.1	s__Azoarcus indigens	82.5888	903	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012911025.1	s__Azoarcus sp012911025	82.5281	875	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	82.2446	773	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	82.1895	623	1483	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	81.8885	658	1483	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	81.8729	640	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCF_001591165.1	s__Thauera butanivorans	81.5483	688	1483	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	81.5287	640	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCA_017302295.1	s__Thauera sp017302295	81.51	645	1483	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	81.4914	463	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	81.1421	648	1483	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	80.5188	689	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910955.1	s__Aromatoleum diolicum	80.1169	599	1483	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	80.0861	578	1483	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910705.1	s__Aromatoleum anaerobium	80.0728	584	1483	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	80.0285	558	1483	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 14:07:38,750] [INFO] GTDB search result was written to GCF_001682385.1_ASM168238v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:38,750] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:38,754] [INFO] DFAST_QC result json was written to GCF_001682385.1_ASM168238v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:38,755] [INFO] DFAST_QC completed!
[2024-01-24 14:07:38,755] [INFO] Total running time: 0h1m51s