[2023-06-19 14:49:04,178] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:49:04,184] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:49:04,184] [INFO] DQC Reference Directory: /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference
[2023-06-19 14:49:05,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:49:05,669] [INFO] Task started: Prodigal
[2023-06-19 14:49:05,669] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0249f56-708b-45aa-8ba1-a133a2145f1d/GCA_018382945.1_ASM1838294v1_genomic.fna.gz | prodigal -d GCA_018382945.1_ASM1838294v1_genomic.fna/cds.fna -a GCA_018382945.1_ASM1838294v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:49:08,759] [INFO] Task succeeded: Prodigal
[2023-06-19 14:49:08,759] [INFO] Task started: HMMsearch
[2023-06-19 14:49:08,759] [INFO] Running command: hmmsearch --tblout GCA_018382945.1_ASM1838294v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/reference_markers.hmm GCA_018382945.1_ASM1838294v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:49:08,928] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:49:08,931] [INFO] Found 6/6 markers.
[2023-06-19 14:49:08,954] [INFO] Query marker FASTA was written to GCA_018382945.1_ASM1838294v1_genomic.fna/markers.fasta
[2023-06-19 14:49:08,955] [INFO] Task started: Blastn
[2023-06-19 14:49:08,955] [INFO] Running command: blastn -query GCA_018382945.1_ASM1838294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/reference_markers.fasta -out GCA_018382945.1_ASM1838294v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:49:09,560] [INFO] Task succeeded: Blastn
[2023-06-19 14:49:09,563] [INFO] Selected 19 target genomes.
[2023-06-19 14:49:09,563] [INFO] Target genome list was writen to GCA_018382945.1_ASM1838294v1_genomic.fna/target_genomes.txt
[2023-06-19 14:49:09,567] [INFO] Task started: fastANI
[2023-06-19 14:49:09,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0249f56-708b-45aa-8ba1-a133a2145f1d/GCA_018382945.1_ASM1838294v1_genomic.fna.gz --refList GCA_018382945.1_ASM1838294v1_genomic.fna/target_genomes.txt --output GCA_018382945.1_ASM1838294v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:49:17,393] [INFO] Task succeeded: fastANI
[2023-06-19 14:49:17,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:49:17,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:49:17,401] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-19 14:49:17,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 14:49:17,401] [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
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000191405.1	729	729	suspected-type	True	95.1048	341	373	95	conclusive
Haemophilus parainfluenzae	strain=ATCC 33392	GCA_000746485.1	729	729	suspected-type	True	95.0575	341	373	95	conclusive
Haemophilus parainfluenzae	strain=FDAARGOS_1000	GCA_016127215.1	729	729	suspected-type	True	94.9357	347	373	95	below_threshold
Haemophilus parainfluenzae	strain=NCTC 7857	GCA_900450845.1	729	729	suspected-type	True	94.9236	343	373	95	below_threshold
Haemophilus pittmaniae	strain=NCTC13334	GCA_900186995.1	249188	249188	type	True	82.3576	189	373	95	below_threshold
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	81.1638	200	373	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	80.519	172	373	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	80.3536	168	373	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	78.8453	177	373	95	below_threshold
Rodentibacter trehalosifermentans	strain=H1987082031	GCA_002000545.1	1908263	1908263	type	True	78.4192	168	373	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:49:17,404] [INFO] DFAST Taxonomy check result was written to GCA_018382945.1_ASM1838294v1_genomic.fna/tc_result.tsv
[2023-06-19 14:49:17,406] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:49:17,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:49:17,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/checkm_data
[2023-06-19 14:49:17,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:49:17,431] [INFO] Task started: CheckM
[2023-06-19 14:49:17,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018382945.1_ASM1838294v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018382945.1_ASM1838294v1_genomic.fna/checkm_input GCA_018382945.1_ASM1838294v1_genomic.fna/checkm_result
[2023-06-19 14:49:32,968] [INFO] Task succeeded: CheckM
[2023-06-19 14:49:32,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 1.94%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-19 14:49:32,993] [INFO] ===== Completeness check finished =====
[2023-06-19 14:49:32,993] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:49:32,993] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018382945.1_ASM1838294v1_genomic.fna/markers.fasta)
[2023-06-19 14:49:32,994] [INFO] Task started: Blastn
[2023-06-19 14:49:32,994] [INFO] Running command: blastn -query GCA_018382945.1_ASM1838294v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce6b34f4-026a-448f-8d49-8af4e800f026/dqc_reference/reference_markers_gtdb.fasta -out GCA_018382945.1_ASM1838294v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:49:33,844] [INFO] Task succeeded: Blastn
[2023-06-19 14:49:33,849] [INFO] Selected 19 target genomes.
[2023-06-19 14:49:33,849] [INFO] Target genome list was writen to GCA_018382945.1_ASM1838294v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:49:33,869] [INFO] Task started: fastANI
[2023-06-19 14:49:33,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0249f56-708b-45aa-8ba1-a133a2145f1d/GCA_018382945.1_ASM1838294v1_genomic.fna.gz --refList GCA_018382945.1_ASM1838294v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018382945.1_ASM1838294v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:49:40,474] [INFO] Task succeeded: fastANI
[2023-06-19 14:49:40,485] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:49:40,485] [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_000191405.1	s__Haemophilus_D parainfluenzae	95.0516	342	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.44	95.10	0.92	0.84	33	conclusive
GCF_003252755.1	s__Haemophilus_D parainfluenzae_N	94.2719	333	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.46	95.02	0.94	0.93	5	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	93.672	331	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
GCA_900756155.1	s__Haemophilus_D sp900756155	93.3643	324	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.93	0.93	2	-
GCF_014931395.1	s__Haemophilus_D sp900764435	93.305	326	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.55	95.23	0.94	0.91	6	-
GCA_905214375.1	s__Haemophilus_D sp905214375	93.2657	298	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	97.05	97.05	0.81	0.81	2	-
GCA_905207935.1	s__Haemophilus_D sp905207935	92.9337	280	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210895.1	s__Haemophilus_D parainfluenzae_A	92.8918	334	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCA_015255025.1	s__Haemophilus_D sp015255025	92.804	264	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.38	95.17	0.91	0.91	3	-
GCA_900756875.1	s__Haemophilus_D sp900756875	92.6928	289	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.91	95.91	0.89	0.89	2	-
GCA_905215245.1	s__Haemophilus_D sp905215245	92.6698	268	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.18	95.12	0.97	0.97	5	-
GCF_014931275.1	s__Haemophilus_D sp900755445	92.3505	329	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.096	96.11	95.22	0.94	0.92	6	-
GCF_003253005.1	s__Haemophilus_D parainfluenzae_M	92.3252	324	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	96.35	95.53	0.93	0.90	14	-
GCA_905205995.1	s__Haemophilus_D sp905205995	92.0572	315	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900638025.1	s__Haemophilus_D parainfluenzae_J	91.3779	311	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.84	95.19	0.91	0.89	5	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	91.2306	242	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.89	95.76	0.75	0.73	3	-
GCF_000827595.2	s__Necropsobacter massiliensis	79.6472	58	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001998825.1	s__Rodentibacter mrazii	78.2749	174	373	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Rodentibacter	95.0	95.11	95.11	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:49:40,487] [INFO] GTDB search result was written to GCA_018382945.1_ASM1838294v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:49:40,488] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:49:40,491] [INFO] DFAST_QC result json was written to GCA_018382945.1_ASM1838294v1_genomic.fna/dqc_result.json
[2023-06-19 14:49:40,491] [INFO] DFAST_QC completed!
[2023-06-19 14:49:40,491] [INFO] Total running time: 0h0m36s