[2024-01-24 11:05:03,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,764] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg21878e82-d239-4325-aa96-9d3dcecf9dbe/GCF_023914155.1_ASM2391415v1_genomic.fna.gz | prodigal -d GCF_023914155.1_ASM2391415v1_genomic.fna/cds.fna -a GCF_023914155.1_ASM2391415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:19,411] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:19,412] [INFO] Task started: HMMsearch
[2024-01-24 11:05:19,412] [INFO] Running command: hmmsearch --tblout GCF_023914155.1_ASM2391415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/reference_markers.hmm GCF_023914155.1_ASM2391415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:19,723] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:19,724] [INFO] Found 6/6 markers.
[2024-01-24 11:05:19,757] [INFO] Query marker FASTA was written to GCF_023914155.1_ASM2391415v1_genomic.fna/markers.fasta
[2024-01-24 11:05:19,757] [INFO] Task started: Blastn
[2024-01-24 11:05:19,757] [INFO] Running command: blastn -query GCF_023914155.1_ASM2391415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/reference_markers.fasta -out GCF_023914155.1_ASM2391415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:20,326] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:20,329] [INFO] Selected 26 target genomes.
[2024-01-24 11:05:20,329] [INFO] Target genome list was writen to GCF_023914155.1_ASM2391415v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:20,351] [INFO] Task started: fastANI
[2024-01-24 11:05:20,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg21878e82-d239-4325-aa96-9d3dcecf9dbe/GCF_023914155.1_ASM2391415v1_genomic.fna.gz --refList GCF_023914155.1_ASM2391415v1_genomic.fna/target_genomes.txt --output GCF_023914155.1_ASM2391415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:41,709] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:41,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:41,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:41,721] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:41,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:41,721] [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
Solitalea longa	strain=HR-AV	GCA_002920915.1	2079460	2079460	type	True	83.6408	934	1385	95	below_threshold
Solitalea canadensis	strain=DSM 3403	GCA_000242635.3	995	995	type	True	78.4883	398	1385	95	below_threshold
Solitalea koreensis	strain=DSM 21342	GCA_900182575.1	543615	543615	type	True	78.3261	172	1385	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	77.0405	51	1385	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	76.5737	67	1385	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	76.4654	66	1385	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	76.4637	60	1385	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	76.41	59	1385	95	below_threshold
Pedobacter zeae	strain=CGMCC 1.15287	GCA_014641575.1	1737356	1737356	type	True	76.3894	61	1385	95	below_threshold
Pedobacter zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	76.3894	61	1385	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	76.3831	53	1385	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	76.3758	60	1385	95	below_threshold
Pseudopedobacter saltans	strain=DSM 12145	GCA_000190735.2	151895	151895	type	True	76.3414	52	1385	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	76.2219	54	1385	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.1328	51	1385	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	75.8986	64	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:41,722] [INFO] DFAST Taxonomy check result was written to GCF_023914155.1_ASM2391415v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:41,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:41,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:41,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/checkm_data
[2024-01-24 11:05:41,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:41,767] [INFO] Task started: CheckM
[2024-01-24 11:05:41,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023914155.1_ASM2391415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023914155.1_ASM2391415v1_genomic.fna/checkm_input GCF_023914155.1_ASM2391415v1_genomic.fna/checkm_result
[2024-01-24 11:06:22,366] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:22,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:22,382] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:22,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:22,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023914155.1_ASM2391415v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:22,383] [INFO] Task started: Blastn
[2024-01-24 11:06:22,383] [INFO] Running command: blastn -query GCF_023914155.1_ASM2391415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80a3728a-3275-4ca0-888c-f8971100cf57/dqc_reference/reference_markers_gtdb.fasta -out GCF_023914155.1_ASM2391415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:23,224] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:23,229] [INFO] Selected 26 target genomes.
[2024-01-24 11:06:23,229] [INFO] Target genome list was writen to GCF_023914155.1_ASM2391415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:23,241] [INFO] Task started: fastANI
[2024-01-24 11:06:23,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg21878e82-d239-4325-aa96-9d3dcecf9dbe/GCF_023914155.1_ASM2391415v1_genomic.fna.gz --refList GCF_023914155.1_ASM2391415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023914155.1_ASM2391415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:44,843] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:44,852] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:44,852] [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_002920915.1	s__Solitalea longa	83.6408	934	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242635.2	s__Solitalea canadensis	78.4883	398	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182575.1	s__Solitalea koreensis	78.3261	172	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Solitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	76.682	65	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_003054145.1	s__Pedobacter sp003054145	76.4726	69	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315595.1	s__Pedobacter miscanthi	76.4637	60	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688475.1	s__Pedobacter sp003688475	76.4624	53	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	76.4154	52	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900215335.1	s__Pedobacter xixiisoli	76.41	59	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000708265.2	s__Pedobacter sp000708265	76.3596	63	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190735.1	s__Pelobium saltans	76.3414	52	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	75.9521	56	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351025.1	s__Mucilaginibacter endophyticus	75.8986	64	1385	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:44,854] [INFO] GTDB search result was written to GCF_023914155.1_ASM2391415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:44,854] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:44,857] [INFO] DFAST_QC result json was written to GCF_023914155.1_ASM2391415v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:44,857] [INFO] DFAST_QC completed!
[2024-01-24 11:06:44,857] [INFO] Total running time: 0h1m41s