[2024-01-24 11:44:38,161] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,163] [INFO] DQC Reference Directory: /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference
[2024-01-24 11:44:41,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,486] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg15e6686d-353d-44fd-90bb-0412bdd686e8/GCF_007625155.1_ASM762515v1_genomic.fna.gz | prodigal -d GCF_007625155.1_ASM762515v1_genomic.fna/cds.fna -a GCF_007625155.1_ASM762515v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:55,942] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:55,942] [INFO] Task started: HMMsearch
[2024-01-24 11:44:55,942] [INFO] Running command: hmmsearch --tblout GCF_007625155.1_ASM762515v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/reference_markers.hmm GCF_007625155.1_ASM762515v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:56,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:56,228] [INFO] Found 6/6 markers.
[2024-01-24 11:44:56,278] [INFO] Query marker FASTA was written to GCF_007625155.1_ASM762515v1_genomic.fna/markers.fasta
[2024-01-24 11:44:56,278] [INFO] Task started: Blastn
[2024-01-24 11:44:56,278] [INFO] Running command: blastn -query GCF_007625155.1_ASM762515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/reference_markers.fasta -out GCF_007625155.1_ASM762515v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:57,242] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:57,246] [INFO] Selected 23 target genomes.
[2024-01-24 11:44:57,247] [INFO] Target genome list was writen to GCF_007625155.1_ASM762515v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:57,295] [INFO] Task started: fastANI
[2024-01-24 11:44:57,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e6686d-353d-44fd-90bb-0412bdd686e8/GCF_007625155.1_ASM762515v1_genomic.fna.gz --refList GCF_007625155.1_ASM762515v1_genomic.fna/target_genomes.txt --output GCF_007625155.1_ASM762515v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:16,341] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:16,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:16,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:16,362] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:45:16,362] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:45:16,363] [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
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	80.3616	685	1447	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	79.2579	552	1447	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.1542	436	1447	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.033	436	1447	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.0042	447	1447	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	78.9815	448	1447	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.9041	459	1447	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	78.8633	465	1447	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.7657	407	1447	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.7082	398	1447	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	78.6625	424	1447	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.6577	429	1447	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.5925	430	1447	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.5348	439	1447	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_003226565.1	41977	41977	type	True	78.3686	368	1447	95	below_threshold
Azoarcus communis	strain=SWub3	GCA_012910815.1	41977	41977	type	True	78.3513	362	1447	95	below_threshold
Aromatoleum petrolei	strain=ToN1	GCA_017894385.1	76116	76116	type	True	78.3488	428	1447	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.2079	352	1447	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.8935	329	1447	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	77.5764	239	1447	95	below_threshold
Pandoraea nosoerga	strain=LMG 31109	GCA_902459585.1	2508296	2508296	type	True	76.5868	171	1447	95	below_threshold
Burkholderia vietnamiensis	strain=FDAARGOS_1488	GCA_020099355.1	60552	60552	type	True	76.3643	189	1447	95	below_threshold
Burkholderia vietnamiensis	strain=LMG 10929	GCA_000959445.1	60552	60552	type	True	76.3549	191	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:16,364] [INFO] DFAST Taxonomy check result was written to GCF_007625155.1_ASM762515v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:16,367] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:16,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:16,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/checkm_data
[2024-01-24 11:45:16,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:16,418] [INFO] Task started: CheckM
[2024-01-24 11:45:16,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007625155.1_ASM762515v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007625155.1_ASM762515v1_genomic.fna/checkm_input GCF_007625155.1_ASM762515v1_genomic.fna/checkm_result
[2024-01-24 11:46:04,539] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:04,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:04,564] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:04,564] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:04,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007625155.1_ASM762515v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:04,565] [INFO] Task started: Blastn
[2024-01-24 11:46:04,565] [INFO] Running command: blastn -query GCF_007625155.1_ASM762515v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga249f7ca-9383-4e1f-b74a-e7e98747f438/dqc_reference/reference_markers_gtdb.fasta -out GCF_007625155.1_ASM762515v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:06,331] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:06,338] [INFO] Selected 10 target genomes.
[2024-01-24 11:46:06,338] [INFO] Target genome list was writen to GCF_007625155.1_ASM762515v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:06,347] [INFO] Task started: fastANI
[2024-01-24 11:46:06,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg15e6686d-353d-44fd-90bb-0412bdd686e8/GCF_007625155.1_ASM762515v1_genomic.fna.gz --refList GCF_007625155.1_ASM762515v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007625155.1_ASM762515v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:16,506] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:16,517] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:16,517] [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_007625155.1	s__Denitromonas halophilus_A	100.0	1443	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007625205.1	s__Denitromonas halophilus	94.4583	1232	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	98.77	98.30	0.95	0.94	5	-
GCA_008501585.1	s__Denitromonas sp008501585	85.6714	1093	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018524365.1	s__Denitromonas sp018524365	85.1206	1051	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010983895.1	s__Denitromonas sp010983895	80.3672	684	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240585.1	s__Thauera sp018240585	78.9339	371	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002354895.1	s__Thauera sp002354895	78.8871	474	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	78.7926	438	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378245.1	s__Aromatoleum toluclasticum	78.6382	431	1447	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	78.5603	434	1447	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 11:46:16,519] [INFO] GTDB search result was written to GCF_007625155.1_ASM762515v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:16,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:16,525] [INFO] DFAST_QC result json was written to GCF_007625155.1_ASM762515v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:16,525] [INFO] DFAST_QC completed!
[2024-01-24 11:46:16,525] [INFO] Total running time: 0h1m38s