[2024-01-24 14:46:34,670] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:34,680] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:34,680] [INFO] DQC Reference Directory: /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference
[2024-01-24 14:46:36,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:36,097] [INFO] Task started: Prodigal
[2024-01-24 14:46:36,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgb418f768-158d-4ac4-994a-05079cbe98c2/GCF_004801295.1_ASM480129v1_genomic.fna.gz | prodigal -d GCF_004801295.1_ASM480129v1_genomic.fna/cds.fna -a GCF_004801295.1_ASM480129v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:51,664] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:51,665] [INFO] Task started: HMMsearch
[2024-01-24 14:46:51,665] [INFO] Running command: hmmsearch --tblout GCF_004801295.1_ASM480129v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/reference_markers.hmm GCF_004801295.1_ASM480129v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:51,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:51,973] [INFO] Found 6/6 markers.
[2024-01-24 14:46:52,013] [INFO] Query marker FASTA was written to GCF_004801295.1_ASM480129v1_genomic.fna/markers.fasta
[2024-01-24 14:46:52,013] [INFO] Task started: Blastn
[2024-01-24 14:46:52,013] [INFO] Running command: blastn -query GCF_004801295.1_ASM480129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/reference_markers.fasta -out GCF_004801295.1_ASM480129v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:53,427] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:53,432] [INFO] Selected 20 target genomes.
[2024-01-24 14:46:53,432] [INFO] Target genome list was writen to GCF_004801295.1_ASM480129v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:53,446] [INFO] Task started: fastANI
[2024-01-24 14:46:53,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgb418f768-158d-4ac4-994a-05079cbe98c2/GCF_004801295.1_ASM480129v1_genomic.fna.gz --refList GCF_004801295.1_ASM480129v1_genomic.fna/target_genomes.txt --output GCF_004801295.1_ASM480129v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:12,913] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:12,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:12,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:12,942] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:12,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:12,942] [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 nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	100.0	1562	1564	95	conclusive
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	85.3456	911	1564	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	82.609	722	1564	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	82.5149	746	1564	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	82.1832	766	1564	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	82.0691	608	1564	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	81.7364	622	1564	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	81.2969	758	1564	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	81.261	623	1564	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	81.2452	753	1564	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	81.2255	623	1564	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	81.1164	568	1564	95	below_threshold
Thauera hydrothermalis	strain=GD-2	GCA_003345255.1	2184083	2184083	type	True	80.8369	613	1564	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.3845	596	1564	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	80.2782	591	1564	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	80.278	606	1564	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.9574	556	1564	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	79.6751	478	1564	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	79.6388	538	1564	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.4923	372	1564	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:12,944] [INFO] DFAST Taxonomy check result was written to GCF_004801295.1_ASM480129v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:12,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:12,946] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:12,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/checkm_data
[2024-01-24 14:47:12,948] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:12,998] [INFO] Task started: CheckM
[2024-01-24 14:47:12,999] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801295.1_ASM480129v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801295.1_ASM480129v1_genomic.fna/checkm_input GCF_004801295.1_ASM480129v1_genomic.fna/checkm_result
[2024-01-24 14:48:12,590] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:12,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:12,700] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:12,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:12,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801295.1_ASM480129v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:12,702] [INFO] Task started: Blastn
[2024-01-24 14:48:12,702] [INFO] Running command: blastn -query GCF_004801295.1_ASM480129v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34ecc4e5-182b-4af8-ab8d-935029dce16a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801295.1_ASM480129v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:14,941] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:14,944] [INFO] Selected 12 target genomes.
[2024-01-24 14:48:14,944] [INFO] Target genome list was writen to GCF_004801295.1_ASM480129v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:14,955] [INFO] Task started: fastANI
[2024-01-24 14:48:14,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgb418f768-158d-4ac4-994a-05079cbe98c2/GCF_004801295.1_ASM480129v1_genomic.fna.gz --refList GCF_004801295.1_ASM480129v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801295.1_ASM480129v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:27,811] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:27,828] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:27,829] [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_004801295.1	s__Thauera_A nasutitermitis	100.0	1562	1564	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_004801305.1	s__Thauera_A rhizosphaerae	85.3443	912	1564	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_014489115.1	s__Thauera_A sp014489115	85.196	828	1564	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_003034845.1	s__Thauera_A sp003034845	83.9653	749	1564	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_001591165.1	s__Thauera butanivorans	82.1966	763	1564	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	82.0281	612	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001682385.1	s__Azoarcus olearius	81.6143	681	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus	95.0	98.77	98.77	0.96	0.96	2	-
GCF_006496635.1	s__Azoarcus sp006496635	81.264	744	1564	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	80.8062	616	1564	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_014822185.1	s__Aromatoleum sp014822185	80.3674	584	1564	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	80.2743	606	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241685.1	s__Zoogloea sp018241685	79.3818	538	1564	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:27,830] [INFO] GTDB search result was written to GCF_004801295.1_ASM480129v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:27,831] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:27,834] [INFO] DFAST_QC result json was written to GCF_004801295.1_ASM480129v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:27,835] [INFO] DFAST_QC completed!
[2024-01-24 14:48:27,835] [INFO] Total running time: 0h1m53s