[2024-01-24 11:20:17,943] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:17,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:17,945] [INFO] DQC Reference Directory: /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference
[2024-01-24 11:20:19,180] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:19,181] [INFO] Task started: Prodigal
[2024-01-24 11:20:19,181] [INFO] Running command: gunzip -c /var/lib/cwl/stgf522f035-a9c5-498c-9dc0-46acfb47e739/GCF_024437735.1_ASM2443773v1_genomic.fna.gz | prodigal -d GCF_024437735.1_ASM2443773v1_genomic.fna/cds.fna -a GCF_024437735.1_ASM2443773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:38,252] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:38,253] [INFO] Task started: HMMsearch
[2024-01-24 11:20:38,253] [INFO] Running command: hmmsearch --tblout GCF_024437735.1_ASM2443773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/reference_markers.hmm GCF_024437735.1_ASM2443773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:38,596] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:38,598] [INFO] Found 6/6 markers.
[2024-01-24 11:20:38,646] [INFO] Query marker FASTA was written to GCF_024437735.1_ASM2443773v1_genomic.fna/markers.fasta
[2024-01-24 11:20:38,647] [INFO] Task started: Blastn
[2024-01-24 11:20:38,647] [INFO] Running command: blastn -query GCF_024437735.1_ASM2443773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/reference_markers.fasta -out GCF_024437735.1_ASM2443773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:39,609] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:39,613] [INFO] Selected 21 target genomes.
[2024-01-24 11:20:39,613] [INFO] Target genome list was writen to GCF_024437735.1_ASM2443773v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:39,619] [INFO] Task started: fastANI
[2024-01-24 11:20:39,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgf522f035-a9c5-498c-9dc0-46acfb47e739/GCF_024437735.1_ASM2443773v1_genomic.fna.gz --refList GCF_024437735.1_ASM2443773v1_genomic.fna/target_genomes.txt --output GCF_024437735.1_ASM2443773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:57,455] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:57,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:57,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:57,474] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:57,474] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:57,474] [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
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	83.6269	1027	1956	95	below_threshold
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	83.6074	1326	1956	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.9563	611	1956	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	78.5577	514	1956	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	78.5261	551	1956	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	78.5204	472	1956	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	78.5196	483	1956	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	78.5044	564	1956	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	78.4045	598	1956	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	78.4	523	1956	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	78.3603	634	1956	95	below_threshold
Pseudoxanthomonas suwonensis	strain=DSM 17175	GCA_010093235.1	314722	314722	suspected-type	True	78.3345	482	1956	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	78.2925	459	1956	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	78.2829	439	1956	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	78.271	412	1956	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	78.1842	580	1956	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	78.1444	501	1956	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	78.1227	394	1956	95	below_threshold
Stenotrophomonas acidaminiphila	strain=JCM 13310	GCA_001431595.1	128780	128780	type	True	77.9737	497	1956	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.8143	612	1956	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.7893	436	1956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:57,476] [INFO] DFAST Taxonomy check result was written to GCF_024437735.1_ASM2443773v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:57,477] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:57,477] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:57,477] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/checkm_data
[2024-01-24 11:20:57,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:57,534] [INFO] Task started: CheckM
[2024-01-24 11:20:57,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024437735.1_ASM2443773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024437735.1_ASM2443773v1_genomic.fna/checkm_input GCF_024437735.1_ASM2443773v1_genomic.fna/checkm_result
[2024-01-24 11:21:57,006] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:57,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:57,030] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:57,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:57,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024437735.1_ASM2443773v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:57,031] [INFO] Task started: Blastn
[2024-01-24 11:21:57,031] [INFO] Running command: blastn -query GCF_024437735.1_ASM2443773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb009fcd9-42a3-4b3e-afd2-bf8a03333ebe/dqc_reference/reference_markers_gtdb.fasta -out GCF_024437735.1_ASM2443773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:58,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:58,909] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:58,909] [INFO] Target genome list was writen to GCF_024437735.1_ASM2443773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:58,948] [INFO] Task started: fastANI
[2024-01-24 11:21:58,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgf522f035-a9c5-498c-9dc0-46acfb47e739/GCF_024437735.1_ASM2443773v1_genomic.fna.gz --refList GCF_024437735.1_ASM2443773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024437735.1_ASM2443773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:11,163] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:11,177] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:22:11,178] [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_004363655.1	s__Tahibacter aquaticus	83.5987	1328	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725155.1	s__Tahibacter sp001725155	83.5076	1238	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCA_013298265.1	s__Tahibacter sp013298265	82.0824	759	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790075.1	s__Tahibacter sp016790075	80.1546	870	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	79.3421	597	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	78.913	650	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	78.5821	719	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	78.5465	515	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	78.3019	472	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001105.1	s__Rhodanobacter sp002001105	78.2958	529	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002951995.1	s__Stenotrophomonas acidaminiphila_A	78.1554	540	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.50	98.36	0.92	0.88	13	-
GCA_003497545.1	s__Arenimonas sp003497545	78.0436	368	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
GCF_008312895.1	s__Luteimonas sp008312895	77.8703	508	1956	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:11,181] [INFO] GTDB search result was written to GCF_024437735.1_ASM2443773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:11,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:11,185] [INFO] DFAST_QC result json was written to GCF_024437735.1_ASM2443773v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:11,186] [INFO] DFAST_QC completed!
[2024-01-24 11:22:11,186] [INFO] Total running time: 0h1m53s