[2024-01-25 19:34:21,106] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:34:21,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:34:21,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference
[2024-01-25 19:34:22,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:34:22,196] [INFO] Task started: Prodigal
[2024-01-25 19:34:22,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b9f6016-65d5-410e-bc93-2df1ed793ecf/GCF_019923725.1_ASM1992372v1_genomic.fna.gz | prodigal -d GCF_019923725.1_ASM1992372v1_genomic.fna/cds.fna -a GCF_019923725.1_ASM1992372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:34:30,590] [INFO] Task succeeded: Prodigal
[2024-01-25 19:34:30,591] [INFO] Task started: HMMsearch
[2024-01-25 19:34:30,591] [INFO] Running command: hmmsearch --tblout GCF_019923725.1_ASM1992372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/reference_markers.hmm GCF_019923725.1_ASM1992372v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:34:30,829] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:34:30,830] [INFO] Found 6/6 markers.
[2024-01-25 19:34:30,859] [INFO] Query marker FASTA was written to GCF_019923725.1_ASM1992372v1_genomic.fna/markers.fasta
[2024-01-25 19:34:30,859] [INFO] Task started: Blastn
[2024-01-25 19:34:30,859] [INFO] Running command: blastn -query GCF_019923725.1_ASM1992372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/reference_markers.fasta -out GCF_019923725.1_ASM1992372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:31,485] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:31,488] [INFO] Selected 23 target genomes.
[2024-01-25 19:34:31,488] [INFO] Target genome list was writen to GCF_019923725.1_ASM1992372v1_genomic.fna/target_genomes.txt
[2024-01-25 19:34:31,494] [INFO] Task started: fastANI
[2024-01-25 19:34:31,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b9f6016-65d5-410e-bc93-2df1ed793ecf/GCF_019923725.1_ASM1992372v1_genomic.fna.gz --refList GCF_019923725.1_ASM1992372v1_genomic.fna/target_genomes.txt --output GCF_019923725.1_ASM1992372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:43,755] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:43,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:43,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:43,763] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:34:43,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:43,763] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	100.0	1061	1064	95	conclusive
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	77.8637	123	1064	95	below_threshold
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	77.682	90	1064	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	77.5698	57	1064	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	77.447	62	1064	95	below_threshold
Bordetella avium	strain=ATCC 35086	GCA_003581385.1	521	521	type	True	77.4385	70	1064	95	below_threshold
Bordetella avium	strain=HAMBI_2160	GCA_003350095.1	521	521	type	True	77.2542	68	1064	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900078335.1	123899	123899	type	True	76.6659	60	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:43,766] [INFO] DFAST Taxonomy check result was written to GCF_019923725.1_ASM1992372v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:43,767] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:43,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:43,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/checkm_data
[2024-01-25 19:34:43,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:43,800] [INFO] Task started: CheckM
[2024-01-25 19:34:43,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019923725.1_ASM1992372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019923725.1_ASM1992372v1_genomic.fna/checkm_input GCF_019923725.1_ASM1992372v1_genomic.fna/checkm_result
[2024-01-25 19:35:12,094] [INFO] Task succeeded: CheckM
[2024-01-25 19:35:12,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:35:12,116] [INFO] ===== Completeness check finished =====
[2024-01-25 19:35:12,116] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:35:12,116] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019923725.1_ASM1992372v1_genomic.fna/markers.fasta)
[2024-01-25 19:35:12,116] [INFO] Task started: Blastn
[2024-01-25 19:35:12,116] [INFO] Running command: blastn -query GCF_019923725.1_ASM1992372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24498143-b028-4d5c-95a3-649d32c03bba/dqc_reference/reference_markers_gtdb.fasta -out GCF_019923725.1_ASM1992372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:13,221] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:13,226] [INFO] Selected 14 target genomes.
[2024-01-25 19:35:13,226] [INFO] Target genome list was writen to GCF_019923725.1_ASM1992372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:35:13,239] [INFO] Task started: fastANI
[2024-01-25 19:35:13,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b9f6016-65d5-410e-bc93-2df1ed793ecf/GCF_019923725.1_ASM1992372v1_genomic.fna.gz --refList GCF_019923725.1_ASM1992372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019923725.1_ASM1992372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:21,437] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:21,445] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:35:21,445] [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_903929925.1	s__NBD-18 sp903929925	83.5076	484	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958565.1	s__NBD-18 sp903958565	83.1715	538	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCA_903903735.1	s__NBD-18 sp903903735	82.7515	440	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292845.1	s__NBD-18 sp002292845	78.4729	125	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	77.937	57	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261355.1	s__Bordetella sp002261355	77.9139	71	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499255.1	s__NBD-18 sp003507735	77.892	122	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.47	99.47	0.95	0.95	2	-
GCA_903821335.1	s__NBD-18 sp903821335	77.7143	115	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.43	99.29	0.86	0.84	5	-
GCA_013205565.1	s__NBD-18 sp013205565	77.5656	140	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847325.1	s__NBD-18 sp903847325	77.2157	130	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865015.1	s__NBD-18 sp903865015	77.1058	117	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:21,447] [INFO] GTDB search result was written to GCF_019923725.1_ASM1992372v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:21,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:21,450] [INFO] DFAST_QC result json was written to GCF_019923725.1_ASM1992372v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:21,450] [INFO] DFAST_QC completed!
[2024-01-25 19:35:21,450] [INFO] Total running time: 0h1m0s