[2024-01-24 15:03:15,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:03:15,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:03:15,076] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference
[2024-01-24 15:03:16,400] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:03:16,401] [INFO] Task started: Prodigal
[2024-01-24 15:03:16,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgba52c2db-2ac1-4e45-ad8d-a17db6c1d0ef/GCF_003967035.1_ASM396703v1_genomic.fna.gz | prodigal -d GCF_003967035.1_ASM396703v1_genomic.fna/cds.fna -a GCF_003967035.1_ASM396703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:26,212] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:26,212] [INFO] Task started: HMMsearch
[2024-01-24 15:03:26,212] [INFO] Running command: hmmsearch --tblout GCF_003967035.1_ASM396703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/reference_markers.hmm GCF_003967035.1_ASM396703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:26,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:26,472] [INFO] Found 6/6 markers.
[2024-01-24 15:03:26,506] [INFO] Query marker FASTA was written to GCF_003967035.1_ASM396703v1_genomic.fna/markers.fasta
[2024-01-24 15:03:26,507] [INFO] Task started: Blastn
[2024-01-24 15:03:26,507] [INFO] Running command: blastn -query GCF_003967035.1_ASM396703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/reference_markers.fasta -out GCF_003967035.1_ASM396703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:27,698] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:27,701] [INFO] Selected 12 target genomes.
[2024-01-24 15:03:27,702] [INFO] Target genome list was writen to GCF_003967035.1_ASM396703v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:27,706] [INFO] Task started: fastANI
[2024-01-24 15:03:27,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgba52c2db-2ac1-4e45-ad8d-a17db6c1d0ef/GCF_003967035.1_ASM396703v1_genomic.fna.gz --refList GCF_003967035.1_ASM396703v1_genomic.fna/target_genomes.txt --output GCF_003967035.1_ASM396703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:37,775] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:37,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:37,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:37,786] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:37,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:37,787] [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
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	84.6569	668	958	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	84.4387	650	958	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	81.5665	584	958	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	81.5111	557	958	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	81.4981	567	958	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	81.2307	566	958	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	80.7965	547	958	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	80.4564	486	958	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.0836	471	958	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.0474	423	958	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	79.9505	507	958	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.6247	361	958	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:37,789] [INFO] DFAST Taxonomy check result was written to GCF_003967035.1_ASM396703v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:37,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:37,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:37,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/checkm_data
[2024-01-24 15:03:37,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:37,820] [INFO] Task started: CheckM
[2024-01-24 15:03:37,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967035.1_ASM396703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967035.1_ASM396703v1_genomic.fna/checkm_input GCF_003967035.1_ASM396703v1_genomic.fna/checkm_result
[2024-01-24 15:04:21,174] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:21,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:21,197] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:21,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:21,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967035.1_ASM396703v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:21,199] [INFO] Task started: Blastn
[2024-01-24 15:04:21,199] [INFO] Running command: blastn -query GCF_003967035.1_ASM396703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fc77726-816a-41d9-be8a-5e052ccf5eb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967035.1_ASM396703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:23,477] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:23,481] [INFO] Selected 15 target genomes.
[2024-01-24 15:04:23,481] [INFO] Target genome list was writen to GCF_003967035.1_ASM396703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:23,503] [INFO] Task started: fastANI
[2024-01-24 15:04:23,504] [INFO] Running command: fastANI --query /var/lib/cwl/stgba52c2db-2ac1-4e45-ad8d-a17db6c1d0ef/GCF_003967035.1_ASM396703v1_genomic.fna.gz --refList GCF_003967035.1_ASM396703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967035.1_ASM396703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:37,265] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:37,279] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:37,279] [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_003967035.1	s__Aerosticca soli	100.0	955	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Aerosticca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148905.1	s__Fulvimonas soli	84.6454	669	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001182895.1	s__Frateuria_B defendens	82.8914	588	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	82.5585	607	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	81.9649	487	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	81.9461	568	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001617365.1	s__Rhodanobacter sp001617365	81.8235	587	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_013620825.1	s__Rhodanobacter sp001899565	81.7109	578	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_012275375.1	s__Dyella sp012275375	81.6064	594	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_002001105.1	s__Rhodanobacter sp002001105	81.5485	568	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970895.1	s__Dyella_A sp018970895	81.5134	512	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279065.1	s__Dyella_A sp002279065	81.4832	570	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000334915.1	s__Dyella_A ginsengisoli	81.4448	587	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428385.1	s__Rhodanobacter sp001428385	81.3689	557	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264315.1	s__Rhodanobacter fulvus	80.4165	490	958	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:37,287] [INFO] GTDB search result was written to GCF_003967035.1_ASM396703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:37,288] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:37,294] [INFO] DFAST_QC result json was written to GCF_003967035.1_ASM396703v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:37,294] [INFO] DFAST_QC completed!
[2024-01-24 15:04:37,294] [INFO] Total running time: 0h1m22s