[2024-01-25 19:11:05,807] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:05,809] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:05,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference
[2024-01-25 19:11:07,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:07,008] [INFO] Task started: Prodigal
[2024-01-25 19:11:07,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgaae298de-2ee8-4bdc-8e1a-81206168f88e/GCF_003730015.1_ASM373001v1_genomic.fna.gz | prodigal -d GCF_003730015.1_ASM373001v1_genomic.fna/cds.fna -a GCF_003730015.1_ASM373001v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:16,764] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:16,765] [INFO] Task started: HMMsearch
[2024-01-25 19:11:16,765] [INFO] Running command: hmmsearch --tblout GCF_003730015.1_ASM373001v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/reference_markers.hmm GCF_003730015.1_ASM373001v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:16,983] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:16,984] [INFO] Found 6/6 markers.
[2024-01-25 19:11:17,010] [INFO] Query marker FASTA was written to GCF_003730015.1_ASM373001v1_genomic.fna/markers.fasta
[2024-01-25 19:11:17,010] [INFO] Task started: Blastn
[2024-01-25 19:11:17,011] [INFO] Running command: blastn -query GCF_003730015.1_ASM373001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/reference_markers.fasta -out GCF_003730015.1_ASM373001v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:17,613] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:17,616] [INFO] Selected 12 target genomes.
[2024-01-25 19:11:17,616] [INFO] Target genome list was writen to GCF_003730015.1_ASM373001v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:17,625] [INFO] Task started: fastANI
[2024-01-25 19:11:17,625] [INFO] Running command: fastANI --query /var/lib/cwl/stgaae298de-2ee8-4bdc-8e1a-81206168f88e/GCF_003730015.1_ASM373001v1_genomic.fna.gz --refList GCF_003730015.1_ASM373001v1_genomic.fna/target_genomes.txt --output GCF_003730015.1_ASM373001v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:26,030] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:26,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:26,031] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:26,039] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:11:26,039] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:11:26,039] [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
Epilithonimonas vandammei	strain=F5649	GCA_003860525.1	2487072	2487072	type	True	94.6414	775	923	95	below_threshold
Epilithonimonas hispanica	strain=KCTC 22104	GCA_003385395.1	358687	358687	type	True	85.8389	634	923	95	below_threshold
Epilithonimonas zeae	strain=DSM 27623	GCA_900141765.1	1416779	1416779	type	True	83.7363	638	923	95	below_threshold
Epilithonimonas arachidiradicis	strain=CCM 8490	GCA_014635405.1	1617282	1617282	type	True	83.5491	611	923	95	below_threshold
Epilithonimonas arachidiradicis	strain=DSM 27620	GCA_003610695.1	1617282	1617282	type	True	83.515	611	923	95	below_threshold
Epilithonimonas caeni	strain=DSM 17710	GCA_000426465.1	365343	365343	type	True	82.5218	605	923	95	below_threshold
Epilithonimonas mollis	strain=DSM 18016	GCA_900142325.1	216903	216903	type	True	82.1898	574	923	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	78.3586	247	923	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	78.234	210	923	95	below_threshold
Chryseobacterium rhizosphaerae	strain=KCTC 22548	GCA_003385455.1	395937	395937	type	True	77.7349	177	923	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.6531	128	923	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.606	127	923	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:26,040] [INFO] DFAST Taxonomy check result was written to GCF_003730015.1_ASM373001v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:26,041] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:26,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:26,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/checkm_data
[2024-01-25 19:11:26,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:26,071] [INFO] Task started: CheckM
[2024-01-25 19:11:26,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003730015.1_ASM373001v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003730015.1_ASM373001v1_genomic.fna/checkm_input GCF_003730015.1_ASM373001v1_genomic.fna/checkm_result
[2024-01-25 19:11:57,652] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:57,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:57,672] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:57,672] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:57,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003730015.1_ASM373001v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:57,672] [INFO] Task started: Blastn
[2024-01-25 19:11:57,672] [INFO] Running command: blastn -query GCF_003730015.1_ASM373001v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a9f0197-ac5b-41a1-87bf-5d60e712e735/dqc_reference/reference_markers_gtdb.fasta -out GCF_003730015.1_ASM373001v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:58,499] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:58,501] [INFO] Selected 11 target genomes.
[2024-01-25 19:11:58,502] [INFO] Target genome list was writen to GCF_003730015.1_ASM373001v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:58,508] [INFO] Task started: fastANI
[2024-01-25 19:11:58,508] [INFO] Running command: fastANI --query /var/lib/cwl/stgaae298de-2ee8-4bdc-8e1a-81206168f88e/GCF_003730015.1_ASM373001v1_genomic.fna.gz --refList GCF_003730015.1_ASM373001v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003730015.1_ASM373001v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:07,027] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:07,035] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:07,035] [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_003730015.1	s__Epilithonimonas hominis	100.0	920	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.55	96.42	0.86	0.85	3	conclusive
GCF_003860525.1	s__Epilithonimonas vandammei	94.6154	776	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	96.28	95.86	0.86	0.84	4	-
GCA_002476905.1	s__Epilithonimonas sp002476905	93.4747	646	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383165.1	s__Epilithonimonas sp002383165	92.7256	729	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002345565.1	s__Epilithonimonas sp002345565	85.8271	592	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385395.1	s__Epilithonimonas hispanica	85.8262	636	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141765.1	s__Epilithonimonas zeae	83.7363	638	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610695.1	s__Epilithonimonas arachidiradicis	83.5298	610	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003248755.1	s__Epilithonimonas sp003248755	83.1134	594	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898785.1	s__Epilithonimonas sp001898785	82.7934	621	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142325.1	s__Epilithonimonas mollis	82.1844	574	923	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Epilithonimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:07,036] [INFO] GTDB search result was written to GCF_003730015.1_ASM373001v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:07,037] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:07,041] [INFO] DFAST_QC result json was written to GCF_003730015.1_ASM373001v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:07,041] [INFO] DFAST_QC completed!
[2024-01-25 19:12:07,041] [INFO] Total running time: 0h1m1s