[2024-01-24 13:49:55,411] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,413] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,413] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference
[2024-01-24 13:49:56,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,628] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,629] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7c804d4-1e9e-4870-be67-d0545bf5d0d9/GCF_009761355.1_ASM976135v1_genomic.fna.gz | prodigal -d GCF_009761355.1_ASM976135v1_genomic.fna/cds.fna -a GCF_009761355.1_ASM976135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:04,210] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:04,211] [INFO] Task started: HMMsearch
[2024-01-24 13:50:04,211] [INFO] Running command: hmmsearch --tblout GCF_009761355.1_ASM976135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/reference_markers.hmm GCF_009761355.1_ASM976135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:04,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:04,491] [INFO] Found 6/6 markers.
[2024-01-24 13:50:04,520] [INFO] Query marker FASTA was written to GCF_009761355.1_ASM976135v1_genomic.fna/markers.fasta
[2024-01-24 13:50:04,521] [INFO] Task started: Blastn
[2024-01-24 13:50:04,521] [INFO] Running command: blastn -query GCF_009761355.1_ASM976135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/reference_markers.fasta -out GCF_009761355.1_ASM976135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:05,296] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:05,300] [INFO] Selected 10 target genomes.
[2024-01-24 13:50:05,301] [INFO] Target genome list was writen to GCF_009761355.1_ASM976135v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:05,305] [INFO] Task started: fastANI
[2024-01-24 13:50:05,305] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c804d4-1e9e-4870-be67-d0545bf5d0d9/GCF_009761355.1_ASM976135v1_genomic.fna.gz --refList GCF_009761355.1_ASM976135v1_genomic.fna/target_genomes.txt --output GCF_009761355.1_ASM976135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:11,661] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:11,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:11,673] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:50:11,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:11,673] [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
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	100.0	863	866	95	conclusive
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	99.9971	864	866	95	conclusive
Testudinibacter aquarius	strain=ELNT2x	GCA_006227605.1	1524974	1524974	type	True	99.8911	767	866	95	conclusive
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	82.3465	597	866	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	82.3121	609	866	95	below_threshold
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	77.5799	158	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,678] [INFO] DFAST Taxonomy check result was written to GCF_009761355.1_ASM976135v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:11,679] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:11,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:11,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/checkm_data
[2024-01-24 13:50:11,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:11,717] [INFO] Task started: CheckM
[2024-01-24 13:50:11,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009761355.1_ASM976135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009761355.1_ASM976135v1_genomic.fna/checkm_input GCF_009761355.1_ASM976135v1_genomic.fna/checkm_result
[2024-01-24 13:50:39,689] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:39,691] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:39,710] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:39,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:39,711] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009761355.1_ASM976135v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:39,712] [INFO] Task started: Blastn
[2024-01-24 13:50:39,712] [INFO] Running command: blastn -query GCF_009761355.1_ASM976135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2b6db24-faff-47a1-af0d-23fffb9be0f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009761355.1_ASM976135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:40,935] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:40,939] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:40,939] [INFO] Target genome list was writen to GCF_009761355.1_ASM976135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:40,959] [INFO] Task started: fastANI
[2024-01-24 13:50:40,959] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c804d4-1e9e-4870-be67-d0545bf5d0d9/GCF_009761355.1_ASM976135v1_genomic.fna.gz --refList GCF_009761355.1_ASM976135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009761355.1_ASM976135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:47,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:47,551] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:47,552] [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_004342725.1	s__Chelonobacter aquarius	99.9971	864	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	conclusive
GCA_006228005.1	s__Chelonobacter sp006228005	92.6801	683	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_900176075.1	s__Chelonobacter testudinis	82.3435	597	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000772535.1	s__Chelonobacter oris	79.412	463	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884965.1	s__Spirabiliibacterium mucosae	77.5799	158	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	-
GCF_004339025.1	s__Volucribacter psittacicida	77.2069	67	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Volucribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379785.1	s__Gallibacterium anatis	77.0186	96	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Gallibacterium	95.0	97.46	96.89	0.84	0.80	28	-
GCF_000827595.2	s__Necropsobacter massiliensis	76.9772	148	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	76.82	82	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999335.1	s__Rodentibacter sp001999335	76.8069	86	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,553] [INFO] GTDB search result was written to GCF_009761355.1_ASM976135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:47,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:47,557] [INFO] DFAST_QC result json was written to GCF_009761355.1_ASM976135v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:47,557] [INFO] DFAST_QC completed!
[2024-01-24 13:50:47,557] [INFO] Total running time: 0h0m52s