[2023-06-18 14:08:12,658] [INFO] DFAST_QC pipeline started.
[2023-06-18 14:08:12,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 14:08:12,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference
[2023-06-18 14:08:14,747] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 14:08:14,748] [INFO] Task started: Prodigal
[2023-06-18 14:08:14,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg099738e6-db5d-4207-b933-54c5222df797/GCA_018006945.1_ASM1800694v1_genomic.fna.gz | prodigal -d GCA_018006945.1_ASM1800694v1_genomic.fna/cds.fna -a GCA_018006945.1_ASM1800694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 14:08:22,133] [INFO] Task succeeded: Prodigal
[2023-06-18 14:08:22,134] [INFO] Task started: HMMsearch
[2023-06-18 14:08:22,134] [INFO] Running command: hmmsearch --tblout GCA_018006945.1_ASM1800694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/reference_markers.hmm GCA_018006945.1_ASM1800694v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 14:08:22,363] [INFO] Task succeeded: HMMsearch
[2023-06-18 14:08:22,365] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg099738e6-db5d-4207-b933-54c5222df797/GCA_018006945.1_ASM1800694v1_genomic.fna.gz]
[2023-06-18 14:08:22,396] [INFO] Query marker FASTA was written to GCA_018006945.1_ASM1800694v1_genomic.fna/markers.fasta
[2023-06-18 14:08:22,396] [INFO] Task started: Blastn
[2023-06-18 14:08:22,396] [INFO] Running command: blastn -query GCA_018006945.1_ASM1800694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/reference_markers.fasta -out GCA_018006945.1_ASM1800694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:08:23,370] [INFO] Task succeeded: Blastn
[2023-06-18 14:08:23,375] [INFO] Selected 20 target genomes.
[2023-06-18 14:08:23,376] [INFO] Target genome list was writen to GCA_018006945.1_ASM1800694v1_genomic.fna/target_genomes.txt
[2023-06-18 14:08:23,378] [INFO] Task started: fastANI
[2023-06-18 14:08:23,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg099738e6-db5d-4207-b933-54c5222df797/GCA_018006945.1_ASM1800694v1_genomic.fna.gz --refList GCA_018006945.1_ASM1800694v1_genomic.fna/target_genomes.txt --output GCA_018006945.1_ASM1800694v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 14:08:38,227] [INFO] Task succeeded: fastANI
[2023-06-18 14:08:38,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 14:08:38,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 14:08:38,250] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 14:08:38,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 14:08:38,251] [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
Zoogloea ramigera	strain=NBRC 15342	GCA_006539865.1	350	350	type	True	83.3679	475	741	95	below_threshold
Zoogloea oleivorans	strain=Buc	GCA_008107625.1	1552750	1552750	type	True	82.9233	489	741	95	below_threshold
Zoogloea dura	strain=G-4-1-14	GCA_012927165.1	2728840	2728840	type	True	82.1762	465	741	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.5974	267	741	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.9614	242	741	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.8977	238	741	95	below_threshold
Azoarcus indigens	strain=DSM 12121	GCA_004361735.1	29545	29545	type	True	78.8961	266	741	95	below_threshold
Azoarcus indigens	strain=VB32	GCA_012910835.1	29545	29545	type	True	78.8134	273	741	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.6795	267	741	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	78.5844	261	741	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.4965	260	741	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	78.4592	214	741	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.4025	267	741	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	78.3777	247	741	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	78.3352	224	741	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	78.2845	230	741	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.0832	224	741	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	77.6811	148	741	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.494	150	741	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.2721	120	741	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 14:08:38,254] [INFO] DFAST Taxonomy check result was written to GCA_018006945.1_ASM1800694v1_genomic.fna/tc_result.tsv
[2023-06-18 14:08:38,255] [INFO] ===== Taxonomy check completed =====
[2023-06-18 14:08:38,255] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 14:08:38,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/checkm_data
[2023-06-18 14:08:38,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 14:08:38,293] [INFO] Task started: CheckM
[2023-06-18 14:08:38,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018006945.1_ASM1800694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018006945.1_ASM1800694v1_genomic.fna/checkm_input GCA_018006945.1_ASM1800694v1_genomic.fna/checkm_result
[2023-06-18 14:09:04,161] [INFO] Task succeeded: CheckM
[2023-06-18 14:09:04,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 14:09:04,187] [INFO] ===== Completeness check finished =====
[2023-06-18 14:09:04,188] [INFO] ===== Start GTDB Search =====
[2023-06-18 14:09:04,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018006945.1_ASM1800694v1_genomic.fna/markers.fasta)
[2023-06-18 14:09:04,188] [INFO] Task started: Blastn
[2023-06-18 14:09:04,189] [INFO] Running command: blastn -query GCA_018006945.1_ASM1800694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1fe12f3-5130-4943-9d6d-d6a6e099c7ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_018006945.1_ASM1800694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 14:09:06,042] [INFO] Task succeeded: Blastn
[2023-06-18 14:09:06,047] [INFO] Selected 17 target genomes.
[2023-06-18 14:09:06,047] [INFO] Target genome list was writen to GCA_018006945.1_ASM1800694v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 14:09:06,052] [INFO] Task started: fastANI
[2023-06-18 14:09:06,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg099738e6-db5d-4207-b933-54c5222df797/GCA_018006945.1_ASM1800694v1_genomic.fna.gz --refList GCA_018006945.1_ASM1800694v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018006945.1_ASM1800694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 14:09:19,667] [INFO] Task succeeded: fastANI
[2023-06-18 14:09:19,688] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 14:09:19,688] [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
GCA_016720685.1	s__Zoogloea sp016720685	85.3728	502	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657735.1	s__Zoogloea sp015657735	83.8091	387	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469605.1	s__Zoogloea sp009469605	83.7275	535	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539865.1	s__Zoogloea ramigera	83.3726	475	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	99.03	99.03	0.93	0.93	2	-
GCF_008107625.1	s__Zoogloea oleivorans	82.9405	488	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789125.1	s__Zoogloea sp016789125	82.7311	399	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241685.1	s__Zoogloea sp018241685	82.3343	470	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241665.1	s__Zoogloea sp018241665	82.3222	461	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927165.1	s__Zoogloea sp012927165	82.2319	461	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241725.1	s__Zoogloea sp018241725	82.0454	466	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026175.1	s__Zoogloea sp009026175	81.8095	449	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302315.1	s__Zoogloea sp017302315	81.5509	391	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	78.7137	227	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983755.1	s__Azonexus sp017983755	78.5967	185	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469585.1	s__Azonexus sp009469585	78.4175	234	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780195.1	s__Azonexus sp018780195	78.2337	173	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008080565.1	s__Azonexus sp008080565	77.9907	212	741	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 14:09:19,691] [INFO] GTDB search result was written to GCA_018006945.1_ASM1800694v1_genomic.fna/result_gtdb.tsv
[2023-06-18 14:09:19,691] [INFO] ===== GTDB Search completed =====
[2023-06-18 14:09:19,696] [INFO] DFAST_QC result json was written to GCA_018006945.1_ASM1800694v1_genomic.fna/dqc_result.json
[2023-06-18 14:09:19,696] [INFO] DFAST_QC completed!
[2023-06-18 14:09:19,696] [INFO] Total running time: 0h1m7s