[2024-01-24 12:47:08,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:08,040] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:08,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference
[2024-01-24 12:47:09,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:09,281] [INFO] Task started: Prodigal
[2024-01-24 12:47:09,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg760b95e9-5e4b-49b1-9dd1-5da5e69c59cf/GCF_000167995.1_ASM16799v1_genomic.fna.gz | prodigal -d GCF_000167995.1_ASM16799v1_genomic.fna/cds.fna -a GCF_000167995.1_ASM16799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:21,545] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:21,546] [INFO] Task started: HMMsearch
[2024-01-24 12:47:21,546] [INFO] Running command: hmmsearch --tblout GCF_000167995.1_ASM16799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/reference_markers.hmm GCF_000167995.1_ASM16799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:21,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:21,916] [INFO] Found 6/6 markers.
[2024-01-24 12:47:21,955] [INFO] Query marker FASTA was written to GCF_000167995.1_ASM16799v1_genomic.fna/markers.fasta
[2024-01-24 12:47:21,956] [INFO] Task started: Blastn
[2024-01-24 12:47:21,956] [INFO] Running command: blastn -query GCF_000167995.1_ASM16799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/reference_markers.fasta -out GCF_000167995.1_ASM16799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:22,848] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:22,851] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:22,851] [INFO] Target genome list was writen to GCF_000167995.1_ASM16799v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:22,856] [INFO] Task started: fastANI
[2024-01-24 12:47:22,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg760b95e9-5e4b-49b1-9dd1-5da5e69c59cf/GCF_000167995.1_ASM16799v1_genomic.fna.gz --refList GCF_000167995.1_ASM16799v1_genomic.fna/target_genomes.txt --output GCF_000167995.1_ASM16799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:35,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:35,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:35,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:35,828] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:35,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:35,828] [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
Yersinia mollaretii	strain=ATCC 43969	GCA_000167995.1	33060	33060	type	True	100.0	1455	1459	95	conclusive
Yersinia mollaretii	strain=ATCC 43969	GCA_013282725.1	33060	33060	type	True	99.9939	1458	1459	95	conclusive
Yersinia aleksiciae	strain=159	GCA_001047675.1	263819	263819	type	True	90.2029	1044	1459	95	below_threshold
Yersinia bercovieri	strain=ATCC 43970	GCA_000167975.1	634	634	type	True	89.726	1122	1459	95	below_threshold
Yersinia bercovieri	strain=ATCC 43970	GCA_013282745.1	634	634	type	True	89.6849	1180	1459	95	below_threshold
Yersinia massiliensis	strain=CCUG 53443	GCA_000312485.1	419257	419257	suspected-type	True	85.4448	1154	1459	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	83.8812	990	1459	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.9734	447	1459	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.9138	363	1459	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.8478	437	1459	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.5941	428	1459	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:35,830] [INFO] DFAST Taxonomy check result was written to GCF_000167995.1_ASM16799v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:35,831] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:35,831] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:35,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/checkm_data
[2024-01-24 12:47:35,833] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:35,881] [INFO] Task started: CheckM
[2024-01-24 12:47:35,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000167995.1_ASM16799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000167995.1_ASM16799v1_genomic.fna/checkm_input GCF_000167995.1_ASM16799v1_genomic.fna/checkm_result
[2024-01-24 12:48:16,930] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:16,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:16,951] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:16,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:16,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000167995.1_ASM16799v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:16,953] [INFO] Task started: Blastn
[2024-01-24 12:48:16,953] [INFO] Running command: blastn -query GCF_000167995.1_ASM16799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6a0ab83-819c-43f3-abd1-2d7e19733285/dqc_reference/reference_markers_gtdb.fasta -out GCF_000167995.1_ASM16799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:18,244] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:18,247] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:18,247] [INFO] Target genome list was writen to GCF_000167995.1_ASM16799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:18,255] [INFO] Task started: fastANI
[2024-01-24 12:48:18,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg760b95e9-5e4b-49b1-9dd1-5da5e69c59cf/GCF_000167995.1_ASM16799v1_genomic.fna.gz --refList GCF_000167995.1_ASM16799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000167995.1_ASM16799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:29,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:29,082] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:29,082] [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_013282725.1	s__Yersinia mollaretii	99.9939	1458	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	conclusive
GCF_001047675.1	s__Yersinia aleksiciae	90.2029	1044	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.22	98.37	0.87	0.82	10	-
GCF_013282745.1	s__Yersinia bercovieri	89.6956	1179	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	-
GCF_000312485.1	s__Yersinia massiliensis	85.4353	1155	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.58	95.54	0.91	0.88	22	-
GCF_001152565.1	s__Yersinia pekkanenii	85.091	1030	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.90	99.90	0.98	0.98	2	-
GCF_001098625.1	s__Yersinia frederiksenii_C	84.8775	1094	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_003600645.1	s__Yersinia rochesterensis	84.7963	1063	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_001123825.1	s__Yersinia kristensenii_C	84.6991	1046	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.60	99.58	0.95	0.93	4	-
GCF_001995075.1	s__Yersinia enterocolitica_F	84.6202	1073	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_009831415.1	s__Yersinia canariae	84.5484	1060	1459	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.93	98.81	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:29,084] [INFO] GTDB search result was written to GCF_000167995.1_ASM16799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:29,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:29,087] [INFO] DFAST_QC result json was written to GCF_000167995.1_ASM16799v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:29,088] [INFO] DFAST_QC completed!
[2024-01-24 12:48:29,088] [INFO] Total running time: 0h1m21s