[2024-01-25 19:57:05,681] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference
[2024-01-25 19:57:06,803] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,804] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,804] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b6640bc-ddef-44e5-bbc8-dca01dffc2a7/GCF_024609805.1_ASM2460980v1_genomic.fna.gz | prodigal -d GCF_024609805.1_ASM2460980v1_genomic.fna/cds.fna -a GCF_024609805.1_ASM2460980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:17,844] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:17,844] [INFO] Task started: HMMsearch
[2024-01-25 19:57:17,844] [INFO] Running command: hmmsearch --tblout GCF_024609805.1_ASM2460980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/reference_markers.hmm GCF_024609805.1_ASM2460980v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:18,106] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:18,107] [INFO] Found 6/6 markers.
[2024-01-25 19:57:18,161] [INFO] Query marker FASTA was written to GCF_024609805.1_ASM2460980v1_genomic.fna/markers.fasta
[2024-01-25 19:57:18,162] [INFO] Task started: Blastn
[2024-01-25 19:57:18,162] [INFO] Running command: blastn -query GCF_024609805.1_ASM2460980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/reference_markers.fasta -out GCF_024609805.1_ASM2460980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:19,135] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:19,137] [INFO] Selected 19 target genomes.
[2024-01-25 19:57:19,137] [INFO] Target genome list was writen to GCF_024609805.1_ASM2460980v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:19,147] [INFO] Task started: fastANI
[2024-01-25 19:57:19,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6640bc-ddef-44e5-bbc8-dca01dffc2a7/GCF_024609805.1_ASM2460980v1_genomic.fna.gz --refList GCF_024609805.1_ASM2460980v1_genomic.fna/target_genomes.txt --output GCF_024609805.1_ASM2460980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:34,150] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:34,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:34,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:34,162] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:34,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:34,162] [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	99.9851	1453	1478	95	conclusive
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	82.6096	1040	1478	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	79.3676	636	1478	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	79.0481	603	1478	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	78.5742	492	1478	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	78.4864	406	1478	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	78.4403	409	1478	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	78.4089	420	1478	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	78.3909	508	1478	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	78.3037	554	1478	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_014656335.1	1169913	1169913	type	True	78.2811	462	1478	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	78.2041	456	1478	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	78.1779	362	1478	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004343305.1	634155	634155	type	True	78.0893	344	1478	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_003732435.1	634155	634155	type	True	78.0545	325	1478	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004798975.1	634155	634155	type	True	78.0014	341	1478	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.9849	321	1478	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	77.9729	306	1478	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	77.9693	341	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:34,164] [INFO] DFAST Taxonomy check result was written to GCF_024609805.1_ASM2460980v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:34,164] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:34,164] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:34,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/checkm_data
[2024-01-25 19:57:34,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:34,220] [INFO] Task started: CheckM
[2024-01-25 19:57:34,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024609805.1_ASM2460980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024609805.1_ASM2460980v1_genomic.fna/checkm_input GCF_024609805.1_ASM2460980v1_genomic.fna/checkm_result
[2024-01-25 19:58:08,907] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:08,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:08,924] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:08,924] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:08,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024609805.1_ASM2460980v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:08,925] [INFO] Task started: Blastn
[2024-01-25 19:58:08,925] [INFO] Running command: blastn -query GCF_024609805.1_ASM2460980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b7048a1-c0b4-4539-bb42-4c767f2567ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_024609805.1_ASM2460980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:10,815] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:10,818] [INFO] Selected 12 target genomes.
[2024-01-25 19:58:10,818] [INFO] Target genome list was writen to GCF_024609805.1_ASM2460980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:10,841] [INFO] Task started: fastANI
[2024-01-25 19:58:10,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6640bc-ddef-44e5-bbc8-dca01dffc2a7/GCF_024609805.1_ASM2460980v1_genomic.fna.gz --refList GCF_024609805.1_ASM2460980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024609805.1_ASM2460980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:24,290] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:24,299] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:58:24,299] [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
GCA_001725155.1	s__Tahibacter sp001725155	89.8388	1216	1478	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	83.7754	706	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363655.1	s__Tahibacter aquaticus	82.6603	1033	1478	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	81.0203	819	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	79.8317	633	1478	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_000953855.2	s__Mizugakiibacter sediminis	79.4685	539	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	79.3882	637	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	79.3764	684	1478	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_002297645.1	s__Dokdonella_A sp002297645	79.3342	526	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCF_014138265.1	s__Dokdonella_A fugitiva_A	79.3221	690	1478	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_004143945.1	s__Dokdonella_A sp004143945	79.1081	546	1478	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_900109915.1	s__Luteibacter sp900109915	77.9372	378	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:24,300] [INFO] GTDB search result was written to GCF_024609805.1_ASM2460980v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:24,301] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:24,305] [INFO] DFAST_QC result json was written to GCF_024609805.1_ASM2460980v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:24,305] [INFO] DFAST_QC completed!
[2024-01-25 19:58:24,305] [INFO] Total running time: 0h1m19s