[2023-06-08 08:48:43,924] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:48:43,935] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:48:43,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference
[2023-06-08 08:48:45,275] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:48:45,279] [INFO] Task started: Prodigal
[2023-06-08 08:48:45,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgecac76d8-c844-4703-bac5-3d00ac784908/GCA_945862175.1_MH-08apr19-317_genomic.fna.gz | prodigal -d GCA_945862175.1_MH-08apr19-317_genomic.fna/cds.fna -a GCA_945862175.1_MH-08apr19-317_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:48:53,034] [INFO] Task succeeded: Prodigal
[2023-06-08 08:48:53,034] [INFO] Task started: HMMsearch
[2023-06-08 08:48:53,035] [INFO] Running command: hmmsearch --tblout GCA_945862175.1_MH-08apr19-317_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/reference_markers.hmm GCA_945862175.1_MH-08apr19-317_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:48:53,368] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:48:53,371] [INFO] Found 6/6 markers.
[2023-06-08 08:48:53,408] [INFO] Query marker FASTA was written to GCA_945862175.1_MH-08apr19-317_genomic.fna/markers.fasta
[2023-06-08 08:48:53,408] [INFO] Task started: Blastn
[2023-06-08 08:48:53,408] [INFO] Running command: blastn -query GCA_945862175.1_MH-08apr19-317_genomic.fna/markers.fasta -db /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/reference_markers.fasta -out GCA_945862175.1_MH-08apr19-317_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:48:54,124] [INFO] Task succeeded: Blastn
[2023-06-08 08:48:54,132] [INFO] Selected 28 target genomes.
[2023-06-08 08:48:54,133] [INFO] Target genome list was writen to GCA_945862175.1_MH-08apr19-317_genomic.fna/target_genomes.txt
[2023-06-08 08:48:54,138] [INFO] Task started: fastANI
[2023-06-08 08:48:54,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgecac76d8-c844-4703-bac5-3d00ac784908/GCA_945862175.1_MH-08apr19-317_genomic.fna.gz --refList GCA_945862175.1_MH-08apr19-317_genomic.fna/target_genomes.txt --output GCA_945862175.1_MH-08apr19-317_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:49:12,794] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:12,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:49:12,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:49:12,806] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:49:12,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:49:12,806] [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	77.8821	164	847	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	77.5905	106	847	95	below_threshold
Jezberella montanilacus	strain=MWH-P2sevCIIIb	GCA_003003055.1	323426	323426	type	True	77.3428	78	847	95	below_threshold
Achromobacter piechaudii	strain=LMG 1873	GCA_902859685.1	72556	72556	type	True	77.0825	53	847	95	below_threshold
Achromobacter piechaudii	strain=NBRC 102461	GCA_001571245.1	72556	72556	type	True	76.9477	52	847	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	76.8093	57	847	95	below_threshold
Achromobacter aestuarii	strain=KS-M25	GCA_009866805.1	2511204	2511204	type	True	76.806	65	847	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	76.782	58	847	95	below_threshold
Bordetella avium	strain=HAMBI_2160	GCA_003350095.1	521	521	type	True	76.7359	66	847	95	below_threshold
Bordetella avium	strain=ATCC 35086	GCA_003581385.1	521	521	type	True	76.7008	67	847	95	below_threshold
Bordetella avium	strain=NCTC12033	GCA_900445835.1	521	521	type	True	76.6683	68	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:49:12,814] [INFO] DFAST Taxonomy check result was written to GCA_945862175.1_MH-08apr19-317_genomic.fna/tc_result.tsv
[2023-06-08 08:49:12,815] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:49:12,815] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:49:12,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/checkm_data
[2023-06-08 08:49:12,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:49:12,850] [INFO] Task started: CheckM
[2023-06-08 08:49:12,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945862175.1_MH-08apr19-317_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945862175.1_MH-08apr19-317_genomic.fna/checkm_input GCA_945862175.1_MH-08apr19-317_genomic.fna/checkm_result
[2023-06-08 08:49:41,682] [INFO] Task succeeded: CheckM
[2023-06-08 08:49:41,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 08:49:41,711] [INFO] ===== Completeness check finished =====
[2023-06-08 08:49:41,711] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:49:41,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945862175.1_MH-08apr19-317_genomic.fna/markers.fasta)
[2023-06-08 08:49:41,712] [INFO] Task started: Blastn
[2023-06-08 08:49:41,713] [INFO] Running command: blastn -query GCA_945862175.1_MH-08apr19-317_genomic.fna/markers.fasta -db /var/lib/cwl/stg2da6d8a0-40c8-4d6f-9cd0-57ce95d82f81/dqc_reference/reference_markers_gtdb.fasta -out GCA_945862175.1_MH-08apr19-317_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:49:42,895] [INFO] Task succeeded: Blastn
[2023-06-08 08:49:42,900] [INFO] Selected 23 target genomes.
[2023-06-08 08:49:42,900] [INFO] Target genome list was writen to GCA_945862175.1_MH-08apr19-317_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:49:42,944] [INFO] Task started: fastANI
[2023-06-08 08:49:42,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgecac76d8-c844-4703-bac5-3d00ac784908/GCA_945862175.1_MH-08apr19-317_genomic.fna.gz --refList GCA_945862175.1_MH-08apr19-317_genomic.fna/target_genomes_gtdb.txt --output GCA_945862175.1_MH-08apr19-317_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:49:56,877] [INFO] Task succeeded: fastANI
[2023-06-08 08:49:56,895] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 08:49:56,895] [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_002292845.1	s__NBD-18 sp002292845	91.0646	538	847	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_002737415.1	s__NBD-18 sp002737415	77.8047	128	847	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_013205565.1	s__NBD-18 sp013205565	77.7216	117	847	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	77.712	139	847	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	77.6295	104	847	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_903847325.1	s__NBD-18 sp903847325	77.5398	123	847	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_903929925.1	s__NBD-18 sp903929925	77.4675	113	847	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_003600685.1	s__Achromobacter spanius_B	77.1976	55	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.56	98.20	0.94	0.92	5	-
GCF_013116765.2	s__Achromobacter deleyi_A	77.1504	54	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865015.1	s__NBD-18 sp903865015	77.0494	122	847	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	77.0402	76	847	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_903903735.1	s__NBD-18 sp903903735	77.0179	97	847	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_001571245.1	s__Achromobacter piechaudii	76.9985	51	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.00	98.18	0.96	0.93	8	-
GCA_903894155.1	s__NBD-18 sp903894155	76.8293	90	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.08	98.85	0.85	0.83	4	-
GCF_900445835.1	s__Bordetella avium	76.7028	67	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.81	99.47	0.98	0.95	26	-
GCF_900496965.1	s__Achromobacter agilis	76.64	55	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261355.1	s__Bordetella sp002261355	76.5733	58	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416405.1	s__Pusillimonas_C sp013416405	76.2354	52	847	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 08:49:56,912] [INFO] GTDB search result was written to GCA_945862175.1_MH-08apr19-317_genomic.fna/result_gtdb.tsv
[2023-06-08 08:49:56,913] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:49:56,920] [INFO] DFAST_QC result json was written to GCA_945862175.1_MH-08apr19-317_genomic.fna/dqc_result.json
[2023-06-08 08:49:56,920] [INFO] DFAST_QC completed!
[2023-06-08 08:49:56,920] [INFO] Total running time: 0h1m13s