[2024-01-24 13:55:18,464] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference
[2024-01-24 13:55:19,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,902] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,902] [INFO] Running command: gunzip -c /var/lib/cwl/stgf850db1d-79b6-466b-9adb-b9081783b75e/GCF_021117405.1_ASM2111740v1_genomic.fna.gz | prodigal -d GCF_021117405.1_ASM2111740v1_genomic.fna/cds.fna -a GCF_021117405.1_ASM2111740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:32,823] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:32,823] [INFO] Task started: HMMsearch
[2024-01-24 13:55:32,823] [INFO] Running command: hmmsearch --tblout GCF_021117405.1_ASM2111740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/reference_markers.hmm GCF_021117405.1_ASM2111740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:33,137] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:33,138] [INFO] Found 6/6 markers.
[2024-01-24 13:55:33,171] [INFO] Query marker FASTA was written to GCF_021117405.1_ASM2111740v1_genomic.fna/markers.fasta
[2024-01-24 13:55:33,172] [INFO] Task started: Blastn
[2024-01-24 13:55:33,172] [INFO] Running command: blastn -query GCF_021117405.1_ASM2111740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/reference_markers.fasta -out GCF_021117405.1_ASM2111740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:34,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:34,169] [INFO] Selected 16 target genomes.
[2024-01-24 13:55:34,169] [INFO] Target genome list was writen to GCF_021117405.1_ASM2111740v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:34,176] [INFO] Task started: fastANI
[2024-01-24 13:55:34,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgf850db1d-79b6-466b-9adb-b9081783b75e/GCF_021117405.1_ASM2111740v1_genomic.fna.gz --refList GCF_021117405.1_ASM2111740v1_genomic.fna/target_genomes.txt --output GCF_021117405.1_ASM2111740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:47,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:47,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:47,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:47,817] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:55:47,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:55:47,818] [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
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	88.6733	1007	1256	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	87.1376	981	1256	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	87.1148	976	1256	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	84.0245	789	1256	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	83.8777	744	1256	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	82.1144	727	1256	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	81.3382	678	1256	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.9366	667	1256	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.9034	553	1256	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.4881	605	1256	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.3976	425	1256	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	75.9012	82	1256	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.2421	137	1256	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.0147	169	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:47,828] [INFO] DFAST Taxonomy check result was written to GCF_021117405.1_ASM2111740v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:47,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:47,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:47,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/checkm_data
[2024-01-24 13:55:47,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:47,883] [INFO] Task started: CheckM
[2024-01-24 13:55:47,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021117405.1_ASM2111740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021117405.1_ASM2111740v1_genomic.fna/checkm_input GCF_021117405.1_ASM2111740v1_genomic.fna/checkm_result
[2024-01-24 13:56:31,705] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:31,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:31,727] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:31,727] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:31,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021117405.1_ASM2111740v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:31,728] [INFO] Task started: Blastn
[2024-01-24 13:56:31,728] [INFO] Running command: blastn -query GCF_021117405.1_ASM2111740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14b67516-25b0-433c-bf6a-0e50f0715758/dqc_reference/reference_markers_gtdb.fasta -out GCF_021117405.1_ASM2111740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:33,391] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:33,394] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:33,395] [INFO] Target genome list was writen to GCF_021117405.1_ASM2111740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:33,437] [INFO] Task started: fastANI
[2024-01-24 13:56:33,438] [INFO] Running command: fastANI --query /var/lib/cwl/stgf850db1d-79b6-466b-9adb-b9081783b75e/GCF_021117405.1_ASM2111740v1_genomic.fna.gz --refList GCF_021117405.1_ASM2111740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021117405.1_ASM2111740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:44,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:44,977] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:56:44,978] [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_017837635.1	s__Frateuria_A sp017837635	88.6733	1007	1256	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_900115705.1	s__Frateuria_A terrea	87.1278	975	1256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013362045.1	s__Frateuria_A sp013362045	86.7269	728	1256	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_003148905.1	s__Fulvimonas soli	84.0142	789	1256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001428405.1	s__Frateuria_A sp001428405	83.8426	804	1256	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_001182895.1	s__Frateuria_B defendens	83.0023	704	1256	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_001617365.1	s__Rhodanobacter sp001617365	82.8548	746	1256	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	82.6158	700	1256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_000334915.1	s__Dyella_A ginsengisoli	82.4683	726	1256	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_018970895.1	s__Dyella_A sp018970895	82.4277	637	1256	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_001641285.1	s__Dyella_A thiooxydans	82.3308	736	1256	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:44,979] [INFO] GTDB search result was written to GCF_021117405.1_ASM2111740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:44,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:44,983] [INFO] DFAST_QC result json was written to GCF_021117405.1_ASM2111740v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:44,983] [INFO] DFAST_QC completed!
[2024-01-24 13:56:44,983] [INFO] Total running time: 0h1m27s