[2023-06-17 06:59:26,785] [INFO] DFAST_QC pipeline started.
[2023-06-17 06:59:26,799] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 06:59:26,799] [INFO] DQC Reference Directory: /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference
[2023-06-17 06:59:28,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 06:59:28,087] [INFO] Task started: Prodigal
[2023-06-17 06:59:28,088] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a1aaff8-c246-44d6-8ea3-f4723fc7faf4/GCA_013205565.1_ASM1320556v1_genomic.fna.gz | prodigal -d GCA_013205565.1_ASM1320556v1_genomic.fna/cds.fna -a GCA_013205565.1_ASM1320556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 06:59:37,073] [INFO] Task succeeded: Prodigal
[2023-06-17 06:59:37,073] [INFO] Task started: HMMsearch
[2023-06-17 06:59:37,074] [INFO] Running command: hmmsearch --tblout GCA_013205565.1_ASM1320556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/reference_markers.hmm GCA_013205565.1_ASM1320556v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 06:59:37,339] [INFO] Task succeeded: HMMsearch
[2023-06-17 06:59:37,341] [INFO] Found 6/6 markers.
[2023-06-17 06:59:37,373] [INFO] Query marker FASTA was written to GCA_013205565.1_ASM1320556v1_genomic.fna/markers.fasta
[2023-06-17 06:59:37,373] [INFO] Task started: Blastn
[2023-06-17 06:59:37,373] [INFO] Running command: blastn -query GCA_013205565.1_ASM1320556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/reference_markers.fasta -out GCA_013205565.1_ASM1320556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 06:59:38,074] [INFO] Task succeeded: Blastn
[2023-06-17 06:59:38,103] [INFO] Selected 21 target genomes.
[2023-06-17 06:59:38,103] [INFO] Target genome list was writen to GCA_013205565.1_ASM1320556v1_genomic.fna/target_genomes.txt
[2023-06-17 06:59:38,110] [INFO] Task started: fastANI
[2023-06-17 06:59:38,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1aaff8-c246-44d6-8ea3-f4723fc7faf4/GCA_013205565.1_ASM1320556v1_genomic.fna.gz --refList GCA_013205565.1_ASM1320556v1_genomic.fna/target_genomes.txt --output GCA_013205565.1_ASM1320556v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 06:59:52,192] [INFO] Task succeeded: fastANI
[2023-06-17 06:59:52,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 06:59:52,193] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 06:59:52,202] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 06:59:52,202] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 06:59:52,202] [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	77.6184	133	966	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	77.0558	96	966	95	below_threshold
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	76.9183	87	966	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	76.4777	50	966	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	75.8966	52	966	95	below_threshold
Achromobacter mucicolens	strain=LMG 26685	GCA_902859725.1	1389922	1389922	type	True	75.8813	53	966	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	75.8276	52	966	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	75.7955	52	966	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	75.7255	53	966	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 06:59:52,204] [INFO] DFAST Taxonomy check result was written to GCA_013205565.1_ASM1320556v1_genomic.fna/tc_result.tsv
[2023-06-17 06:59:52,205] [INFO] ===== Taxonomy check completed =====
[2023-06-17 06:59:52,205] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 06:59:52,206] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/checkm_data
[2023-06-17 06:59:52,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 06:59:52,245] [INFO] Task started: CheckM
[2023-06-17 06:59:52,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013205565.1_ASM1320556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013205565.1_ASM1320556v1_genomic.fna/checkm_input GCA_013205565.1_ASM1320556v1_genomic.fna/checkm_result
[2023-06-17 07:00:23,988] [INFO] Task succeeded: CheckM
[2023-06-17 07:00:23,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 07:00:24,013] [INFO] ===== Completeness check finished =====
[2023-06-17 07:00:24,013] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:00:24,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013205565.1_ASM1320556v1_genomic.fna/markers.fasta)
[2023-06-17 07:00:24,014] [INFO] Task started: Blastn
[2023-06-17 07:00:24,014] [INFO] Running command: blastn -query GCA_013205565.1_ASM1320556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcecbfee9-dfcb-4a81-91a3-abd66bc41a21/dqc_reference/reference_markers_gtdb.fasta -out GCA_013205565.1_ASM1320556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:00:25,176] [INFO] Task succeeded: Blastn
[2023-06-17 07:00:25,181] [INFO] Selected 14 target genomes.
[2023-06-17 07:00:25,182] [INFO] Target genome list was writen to GCA_013205565.1_ASM1320556v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:00:25,188] [INFO] Task started: fastANI
[2023-06-17 07:00:25,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a1aaff8-c246-44d6-8ea3-f4723fc7faf4/GCA_013205565.1_ASM1320556v1_genomic.fna.gz --refList GCA_013205565.1_ASM1320556v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013205565.1_ASM1320556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:00:34,706] [INFO] Task succeeded: fastANI
[2023-06-17 07:00:34,719] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:00:34,719] [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_013205565.1	s__NBD-18 sp013205565	100.0	951	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002737415.1	s__NBD-18 sp002737415	93.5934	841	966	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_903932425.1	s__NBD-18 sp903932425	80.3683	496	966	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_903924715.1	s__NBD-18 sp903924715	79.9442	335	966	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	77.8527	122	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.16	98.92	0.86	0.85	5	-
GCF_010499255.1	s__NBD-18 sp003507735	77.0558	96	966	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_903903735.1	s__NBD-18 sp903903735	76.7053	85	966	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_002261345.1	s__Bordetella_A sp002261345	76.1827	55	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_014490035.1	s__Achromobacter bronchisepticus_A	76.1121	52	966	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0106	99.75	98.99	0.98	0.93	5	-
--------------------------------------------------------------------------------
[2023-06-17 07:00:34,722] [INFO] GTDB search result was written to GCA_013205565.1_ASM1320556v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:00:34,722] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:00:34,727] [INFO] DFAST_QC result json was written to GCA_013205565.1_ASM1320556v1_genomic.fna/dqc_result.json
[2023-06-17 07:00:34,728] [INFO] DFAST_QC completed!
[2023-06-17 07:00:34,728] [INFO] Total running time: 0h1m8s