[2024-01-24 12:54:22,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference
[2024-01-24 12:54:24,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:24,039] [INFO] Task started: Prodigal
[2024-01-24 12:54:24,039] [INFO] Running command: gunzip -c /var/lib/cwl/stg72fd9628-ed3d-4a22-8b5c-99dc5a19c6ec/GCF_024158035.1_ASM2415803v1_genomic.fna.gz | prodigal -d GCF_024158035.1_ASM2415803v1_genomic.fna/cds.fna -a GCF_024158035.1_ASM2415803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:37,994] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:37,994] [INFO] Task started: HMMsearch
[2024-01-24 12:54:37,994] [INFO] Running command: hmmsearch --tblout GCF_024158035.1_ASM2415803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/reference_markers.hmm GCF_024158035.1_ASM2415803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:38,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:38,306] [INFO] Found 6/6 markers.
[2024-01-24 12:54:38,347] [INFO] Query marker FASTA was written to GCF_024158035.1_ASM2415803v1_genomic.fna/markers.fasta
[2024-01-24 12:54:38,347] [INFO] Task started: Blastn
[2024-01-24 12:54:38,347] [INFO] Running command: blastn -query GCF_024158035.1_ASM2415803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/reference_markers.fasta -out GCF_024158035.1_ASM2415803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:39,417] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:39,421] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:39,422] [INFO] Target genome list was writen to GCF_024158035.1_ASM2415803v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:39,431] [INFO] Task started: fastANI
[2024-01-24 12:54:39,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg72fd9628-ed3d-4a22-8b5c-99dc5a19c6ec/GCF_024158035.1_ASM2415803v1_genomic.fna.gz --refList GCF_024158035.1_ASM2415803v1_genomic.fna/target_genomes.txt --output GCF_024158035.1_ASM2415803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:52,947] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:52,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:52,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:52,965] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:52,965] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:52,966] [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	83.9187	835	1463	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	83.8418	790	1463	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	82.8548	831	1463	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	82.7267	767	1463	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	82.4159	750	1463	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	82.337	767	1463	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	82.285	767	1463	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	82.229	731	1463	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	81.6751	716	1463	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	81.1412	718	1463	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.9472	720	1463	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.8375	606	1463	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.4852	663	1463	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	79.5696	555	1463	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.4796	436	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:52,968] [INFO] DFAST Taxonomy check result was written to GCF_024158035.1_ASM2415803v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:52,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:52,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:52,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/checkm_data
[2024-01-24 12:54:52,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:53,016] [INFO] Task started: CheckM
[2024-01-24 12:54:53,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024158035.1_ASM2415803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024158035.1_ASM2415803v1_genomic.fna/checkm_input GCF_024158035.1_ASM2415803v1_genomic.fna/checkm_result
[2024-01-24 12:55:41,420] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:41,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:41,458] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:41,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:41,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024158035.1_ASM2415803v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:41,459] [INFO] Task started: Blastn
[2024-01-24 12:55:41,459] [INFO] Running command: blastn -query GCF_024158035.1_ASM2415803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3b11cb-05e5-49eb-9dad-08b6c2452e8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024158035.1_ASM2415803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:43,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:43,587] [INFO] Selected 10 target genomes.
[2024-01-24 12:55:43,587] [INFO] Target genome list was writen to GCF_024158035.1_ASM2415803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:43,596] [INFO] Task started: fastANI
[2024-01-24 12:55:43,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg72fd9628-ed3d-4a22-8b5c-99dc5a19c6ec/GCF_024158035.1_ASM2415803v1_genomic.fna.gz --refList GCF_024158035.1_ASM2415803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024158035.1_ASM2415803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:53,101] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:53,114] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:55:53,114] [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_001641285.1	s__Dyella_A thiooxydans	93.5376	1249	1463	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_000334915.1	s__Dyella_A ginsengisoli	93.1423	1210	1463	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	90.1378	1112	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018970895.1	s__Dyella_A sp018970895	88.9778	920	1463	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_001428405.1	s__Frateuria_A sp001428405	83.5683	845	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001617365.1	s__Rhodanobacter sp001617365	83.1656	786	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCA_013362045.1	s__Frateuria_A sp013362045	83.0577	615	1463	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	83.0508	702	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	82.5999	781	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_017837635.1	s__Frateuria_A sp017837635	82.2296	731	1463	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:53,116] [INFO] GTDB search result was written to GCF_024158035.1_ASM2415803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:53,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:53,120] [INFO] DFAST_QC result json was written to GCF_024158035.1_ASM2415803v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:53,120] [INFO] DFAST_QC completed!
[2024-01-24 12:55:53,120] [INFO] Total running time: 0h1m31s