[2024-01-24 10:47:06,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,602] [INFO] DQC Reference Directory: /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference
[2024-01-24 10:47:12,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,828] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg16bcbbf8-ea1a-44a7-88cb-145856ca4a3c/GCF_015356115.1_ASM1535611v1_genomic.fna.gz | prodigal -d GCF_015356115.1_ASM1535611v1_genomic.fna/cds.fna -a GCF_015356115.1_ASM1535611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:18,883] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:18,883] [INFO] Task started: HMMsearch
[2024-01-24 10:47:18,883] [INFO] Running command: hmmsearch --tblout GCF_015356115.1_ASM1535611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/reference_markers.hmm GCF_015356115.1_ASM1535611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:19,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:19,135] [INFO] Found 6/6 markers.
[2024-01-24 10:47:19,162] [INFO] Query marker FASTA was written to GCF_015356115.1_ASM1535611v1_genomic.fna/markers.fasta
[2024-01-24 10:47:19,162] [INFO] Task started: Blastn
[2024-01-24 10:47:19,163] [INFO] Running command: blastn -query GCF_015356115.1_ASM1535611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/reference_markers.fasta -out GCF_015356115.1_ASM1535611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,876] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,880] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:19,881] [INFO] Target genome list was writen to GCF_015356115.1_ASM1535611v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:21,056] [INFO] Task started: fastANI
[2024-01-24 10:47:21,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg16bcbbf8-ea1a-44a7-88cb-145856ca4a3c/GCF_015356115.1_ASM1535611v1_genomic.fna.gz --refList GCF_015356115.1_ASM1535611v1_genomic.fna/target_genomes.txt --output GCF_015356115.1_ASM1535611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:33,564] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:33,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:33,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:33,582] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:33,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:33,582] [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
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	100.0	829	832	95	conclusive
Rodentibacter myodis	strain=Ac151	GCA_001999305.1	1907939	1907939	type	True	82.5282	564	832	95	below_threshold
Rodentibacter pneumotropicus	strain=ATCC 35149	GCA_000730685.1	758	758	type	True	80.6739	470	832	95	below_threshold
Rodentibacter ratti	strain=F75	GCA_002000485.1	1906745	1906745	type	True	80.3384	440	832	95	below_threshold
Rodentibacter pneumotropicus	strain=DSM 21403	GCA_000379905.1	758	758	type	True	80.3264	468	832	95	below_threshold
Rodentibacter mrazii	strain=Ppn418	GCA_001998825.1	1908257	1908257	type	True	80.2221	457	832	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	80.1004	437	832	95	below_threshold
Rodentibacter rarus	strain=CCUG 17206	GCA_001998965.1	1908260	1908260	type	True	80.0846	410	832	95	below_threshold
Rodentibacter heidelbergensis	strain=Ac69	GCA_002000125.1	1908258	1908258	type	True	79.884	417	832	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	79.5611	330	832	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	79.3762	327	832	95	below_threshold
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	79.244	309	832	95	below_threshold
Aggregatibacter segnis	strain=ATCC 33393	GCA_000185305.1	739	739	type	True	78.546	200	832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:33,584] [INFO] DFAST Taxonomy check result was written to GCF_015356115.1_ASM1535611v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:33,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:33,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:33,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/checkm_data
[2024-01-24 10:47:33,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:33,616] [INFO] Task started: CheckM
[2024-01-24 10:47:33,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015356115.1_ASM1535611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015356115.1_ASM1535611v1_genomic.fna/checkm_input GCF_015356115.1_ASM1535611v1_genomic.fna/checkm_result
[2024-01-24 10:47:58,434] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:58,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:58,456] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:58,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:58,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015356115.1_ASM1535611v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:58,458] [INFO] Task started: Blastn
[2024-01-24 10:47:58,458] [INFO] Running command: blastn -query GCF_015356115.1_ASM1535611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36a67b3-fd97-4951-a35f-8d527e8db051/dqc_reference/reference_markers_gtdb.fasta -out GCF_015356115.1_ASM1535611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,341] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,345] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:59,345] [INFO] Target genome list was writen to GCF_015356115.1_ASM1535611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:59,957] [INFO] Task started: fastANI
[2024-01-24 10:47:59,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg16bcbbf8-ea1a-44a7-88cb-145856ca4a3c/GCF_015356115.1_ASM1535611v1_genomic.fna.gz --refList GCF_015356115.1_ASM1535611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015356115.1_ASM1535611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:09,354] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:09,379] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:09,380] [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_015356115.1	s__Rodentibacter sp015356115	100.0	830	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001999305.1	s__Rodentibacter myodis	82.5261	565	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000485.1	s__Rodentibacter ratti	80.3386	440	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	96.24	96.11	0.85	0.81	4	-
GCF_000379905.1	s__Rodentibacter pneumotropicus	80.3262	468	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.90	97.98	0.93	0.87	18	-
GCF_001999285.1	s__Rodentibacter sp001999285	80.2371	448	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	97.96	97.96	0.90	0.90	3	-
GCF_001998825.1	s__Rodentibacter mrazii	80.2179	458	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
GCF_001019715.1	s__Rodentibacter heylii	80.1518	488	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.70	95.96	0.96	0.90	9	-
GCF_002000545.1	s__Rodentibacter trehalosifermentans	80.1136	436	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	98.00	97.91	0.88	0.88	3	-
GCF_001999425.1	s__Rodentibacter sp001999425	80.0907	481	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901420285.1	s__Rodentibacter sp901420285	79.9408	364	832	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	79.9366	472	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000125.1	s__Rodentibacter heidelbergensis	79.8317	421	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352385.1	s__Haemophilus haemolyticus_I	79.7975	326	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.71	95.22	0.89	0.82	17	-
GCF_000222025.1	s__Haemophilus haemolyticus_G	79.5238	323	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457655.1	s__Haemophilus influenzae	79.4911	329	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9609	97.88	97.07	0.94	0.87	511	-
GCF_001679485.1	s__Haemophilus_D sp001679485	79.1045	325	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	95.82	95.82	0.90	0.90	2	-
GCA_015255025.1	s__Haemophilus_D sp015255025	78.2531	239	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,381] [INFO] GTDB search result was written to GCF_015356115.1_ASM1535611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:09,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:09,386] [INFO] DFAST_QC result json was written to GCF_015356115.1_ASM1535611v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:09,386] [INFO] DFAST_QC completed!
[2024-01-24 10:48:09,386] [INFO] Total running time: 0h1m3s