[2023-06-19 12:33:01,508] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:33:01,511] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:33:01,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference
[2023-06-19 12:33:02,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:33:02,802] [INFO] Task started: Prodigal
[2023-06-19 12:33:02,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgee199681-57ce-4040-b566-3ca6f19bffe6/GCA_018333815.1_ASM1833381v1_genomic.fna.gz | prodigal -d GCA_018333815.1_ASM1833381v1_genomic.fna/cds.fna -a GCA_018333815.1_ASM1833381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:33:08,588] [INFO] Task succeeded: Prodigal
[2023-06-19 12:33:08,588] [INFO] Task started: HMMsearch
[2023-06-19 12:33:08,589] [INFO] Running command: hmmsearch --tblout GCA_018333815.1_ASM1833381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/reference_markers.hmm GCA_018333815.1_ASM1833381v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:33:08,915] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:33:08,916] [INFO] Found 6/6 markers.
[2023-06-19 12:33:08,946] [INFO] Query marker FASTA was written to GCA_018333815.1_ASM1833381v1_genomic.fna/markers.fasta
[2023-06-19 12:33:08,947] [INFO] Task started: Blastn
[2023-06-19 12:33:08,947] [INFO] Running command: blastn -query GCA_018333815.1_ASM1833381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/reference_markers.fasta -out GCA_018333815.1_ASM1833381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:33:10,084] [INFO] Task succeeded: Blastn
[2023-06-19 12:33:10,089] [INFO] Selected 21 target genomes.
[2023-06-19 12:33:10,090] [INFO] Target genome list was writen to GCA_018333815.1_ASM1833381v1_genomic.fna/target_genomes.txt
[2023-06-19 12:33:10,096] [INFO] Task started: fastANI
[2023-06-19 12:33:10,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgee199681-57ce-4040-b566-3ca6f19bffe6/GCA_018333815.1_ASM1833381v1_genomic.fna.gz --refList GCA_018333815.1_ASM1833381v1_genomic.fna/target_genomes.txt --output GCA_018333815.1_ASM1833381v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:33:26,734] [INFO] Task succeeded: fastANI
[2023-06-19 12:33:26,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:33:26,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:33:26,762] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:33:26,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:33:26,762] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	81.2043	327	660	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	81.0776	333	660	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.2578	277	660	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.0882	281	660	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	78.7366	291	660	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.7237	249	660	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.714	246	660	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.6918	248	660	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.6731	255	660	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.3784	204	660	95	below_threshold
Aromatoleum bremense	strain=PbN1	GCA_017894365.1	76115	76115	type	True	78.3194	242	660	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.2738	224	660	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.2028	223	660	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.1088	202	660	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	78.0368	185	660	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	77.9745	196	660	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	77.9513	198	660	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	77.948	204	660	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	77.8542	258	660	95	below_threshold
Chromobacterium violaceum	strain=ATCC 12472	GCA_000007705.1	536	536	type	True	77.1535	170	660	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.0793	143	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:33:26,788] [INFO] DFAST Taxonomy check result was written to GCA_018333815.1_ASM1833381v1_genomic.fna/tc_result.tsv
[2023-06-19 12:33:26,789] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:33:26,789] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:33:26,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/checkm_data
[2023-06-19 12:33:26,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:33:26,840] [INFO] Task started: CheckM
[2023-06-19 12:33:26,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018333815.1_ASM1833381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018333815.1_ASM1833381v1_genomic.fna/checkm_input GCA_018333815.1_ASM1833381v1_genomic.fna/checkm_result
[2023-06-19 12:33:50,748] [INFO] Task succeeded: CheckM
[2023-06-19 12:33:50,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:33:50,771] [INFO] ===== Completeness check finished =====
[2023-06-19 12:33:50,771] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:33:50,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018333815.1_ASM1833381v1_genomic.fna/markers.fasta)
[2023-06-19 12:33:50,772] [INFO] Task started: Blastn
[2023-06-19 12:33:50,772] [INFO] Running command: blastn -query GCA_018333815.1_ASM1833381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ffa2e54-adad-4546-be60-c87ffd64449d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018333815.1_ASM1833381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:33:52,813] [INFO] Task succeeded: Blastn
[2023-06-19 12:33:52,818] [INFO] Selected 14 target genomes.
[2023-06-19 12:33:52,818] [INFO] Target genome list was writen to GCA_018333815.1_ASM1833381v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:33:52,828] [INFO] Task started: fastANI
[2023-06-19 12:33:52,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgee199681-57ce-4040-b566-3ca6f19bffe6/GCA_018333815.1_ASM1833381v1_genomic.fna.gz --refList GCA_018333815.1_ASM1833381v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018333815.1_ASM1833381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:34:01,057] [INFO] Task succeeded: fastANI
[2023-06-19 12:34:01,074] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:34:01,074] [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_018333815.1	s__UBA2250 sp018333815	100.0	657	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002347285.1	s__UBA2250 sp002347285	83.65	396	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330945.1	s__UBA2250 sp011330945	82.2912	411	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.90	99.90	0.95	0.95	2	-
GCA_004323595.1	s__UBA2250 sp004323595	81.332	387	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865015.1	s__Sulfurisoma sediminicola	81.2041	327	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	99.99	99.99	0.99	0.99	2	-
GCA_013426785.1	s__UBA2250 sp013426785	80.9191	322	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003966565.1	s__UBA2250 sp003966565	80.8979	381	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347405.1	s__UBA2250 sp002347405	80.2293	343	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.89	99.89	0.96	0.96	2	-
GCA_011391215.1	s__UBA2250 sp011391215	79.6608	257	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791905.1	s__UBA2250 sp013791905	79.6496	343	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	100.00	99.98	1.00	0.99	7	-
GCF_007833355.1	s__Denitratisoma sp007833355	79.315	281	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903950295.1	s__UBA2250 sp903950295	79.3138	214	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026675.1	s__Sulfuritalea sp012026675	79.0922	212	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428465.1	s__Chitinimonas koreensis	77.8669	257	660	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:34:01,076] [INFO] GTDB search result was written to GCA_018333815.1_ASM1833381v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:34:01,077] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:34:01,082] [INFO] DFAST_QC result json was written to GCA_018333815.1_ASM1833381v1_genomic.fna/dqc_result.json
[2023-06-19 12:34:01,083] [INFO] DFAST_QC completed!
[2023-06-19 12:34:01,083] [INFO] Total running time: 0h0m60s