[2024-01-24 12:07:06,570] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference
[2024-01-24 12:07:07,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,822] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,823] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b3d8e3d-b509-4d4d-956c-0ab8c18bdf8a/GCF_030160295.1_ASM3016029v1_genomic.fna.gz | prodigal -d GCF_030160295.1_ASM3016029v1_genomic.fna/cds.fna -a GCF_030160295.1_ASM3016029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:26,577] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:26,578] [INFO] Task started: HMMsearch
[2024-01-24 12:07:26,578] [INFO] Running command: hmmsearch --tblout GCF_030160295.1_ASM3016029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/reference_markers.hmm GCF_030160295.1_ASM3016029v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:26,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:26,920] [INFO] Found 6/6 markers.
[2024-01-24 12:07:26,966] [INFO] Query marker FASTA was written to GCF_030160295.1_ASM3016029v1_genomic.fna/markers.fasta
[2024-01-24 12:07:26,967] [INFO] Task started: Blastn
[2024-01-24 12:07:26,967] [INFO] Running command: blastn -query GCF_030160295.1_ASM3016029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/reference_markers.fasta -out GCF_030160295.1_ASM3016029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:27,870] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:27,873] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:27,874] [INFO] Target genome list was writen to GCF_030160295.1_ASM3016029v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:27,879] [INFO] Task started: fastANI
[2024-01-24 12:07:27,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3d8e3d-b509-4d4d-956c-0ab8c18bdf8a/GCF_030160295.1_ASM3016029v1_genomic.fna.gz --refList GCF_030160295.1_ASM3016029v1_genomic.fna/target_genomes.txt --output GCF_030160295.1_ASM3016029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:40,783] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:40,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:40,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:40,798] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:40,798] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:40,798] [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
Dyella nitratireducens	strain=CGMCC 1.15439	GCA_014642835.1	1849580	1849580	type	True	82.9303	1186	1754	95	below_threshold
Dyella choica	strain=4 M-K27	GCA_003977665.1	1927959	1927959	type	True	82.416	1090	1754	95	below_threshold
Dyella monticola	strain=4 G-K06	GCA_003363155.1	1927958	1927958	type	True	81.4658	887	1754	95	below_threshold
Dyella psychrodurans	strain=4MSK11	GCA_003363265.1	1927960	1927960	type	True	81.3802	833	1754	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.375	915	1754	95	below_threshold
Dyella mobilis	strain=DHON07	GCA_016904945.1	1849582	1849582	type	True	81.1481	842	1754	95	below_threshold
Dyella flava	strain=DHOC52	GCA_016904955.1	1920170	1920170	type	True	81.0999	806	1754	95	below_threshold
Dyella caseinilytica	strain=CGMCC 1.15434	GCA_014642815.1	1849581	1849581	type	True	80.6562	831	1754	95	below_threshold
Dyella caseinilytica	strain=DHOB09	GCA_016865235.1	1849581	1849581	type	True	80.6511	828	1754	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	79.6007	485	1754	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.4135	607	1754	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	79.1927	460	1754	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.7887	220	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:40,800] [INFO] DFAST Taxonomy check result was written to GCF_030160295.1_ASM3016029v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:40,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:40,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:40,801] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/checkm_data
[2024-01-24 12:07:40,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:40,851] [INFO] Task started: CheckM
[2024-01-24 12:07:40,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160295.1_ASM3016029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160295.1_ASM3016029v1_genomic.fna/checkm_input GCF_030160295.1_ASM3016029v1_genomic.fna/checkm_result
[2024-01-24 12:08:36,501] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:36,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:36,528] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:36,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:36,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160295.1_ASM3016029v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:36,529] [INFO] Task started: Blastn
[2024-01-24 12:08:36,529] [INFO] Running command: blastn -query GCF_030160295.1_ASM3016029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4efbeb7d-5fcc-4c84-a780-8c987f98aff4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160295.1_ASM3016029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:38,236] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:38,240] [INFO] Selected 10 target genomes.
[2024-01-24 12:08:38,240] [INFO] Target genome list was writen to GCF_030160295.1_ASM3016029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:38,248] [INFO] Task started: fastANI
[2024-01-24 12:08:38,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3d8e3d-b509-4d4d-956c-0ab8c18bdf8a/GCF_030160295.1_ASM3016029v1_genomic.fna.gz --refList GCF_030160295.1_ASM3016029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160295.1_ASM3016029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:49,686] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:49,697] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:49,698] [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_014873315.1	s__Dyella_B sp014873315	83.2066	1049	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642835.1	s__Dyella_B nitratireducens	82.9223	1186	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977665.1	s__Dyella_B choica	82.4335	1088	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363155.1	s__Dyella_B monticola	81.4782	885	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863405.1	s__Dyella_B sp014863405	81.3734	915	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904945.1	s__Dyella_B mobilis	81.1325	844	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904955.1	s__Dyella_B flava	81.0891	806	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865235.1	s__Dyella_B caseinilytica	80.6506	828	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903970555.1	s__Dyella_B sp903970555	80.3905	694	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012275375.1	s__Dyella sp012275375	79.9096	660	1754	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:49,699] [INFO] GTDB search result was written to GCF_030160295.1_ASM3016029v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:49,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:49,704] [INFO] DFAST_QC result json was written to GCF_030160295.1_ASM3016029v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:49,704] [INFO] DFAST_QC completed!
[2024-01-24 12:08:49,704] [INFO] Total running time: 0h1m43s