[2024-01-24 15:06:36,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference
[2024-01-24 15:06:38,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,417] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,418] [INFO] Running command: gunzip -c /var/lib/cwl/stgfdab3ef4-d70c-4b19-9131-8ceb93a48b0e/GCF_004368535.1_ASM436853v1_genomic.fna.gz | prodigal -d GCF_004368535.1_ASM436853v1_genomic.fna/cds.fna -a GCF_004368535.1_ASM436853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:42,798] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:42,799] [INFO] Task started: HMMsearch
[2024-01-24 15:06:42,799] [INFO] Running command: hmmsearch --tblout GCF_004368535.1_ASM436853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/reference_markers.hmm GCF_004368535.1_ASM436853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:43,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:43,089] [INFO] Found 6/6 markers.
[2024-01-24 15:06:43,117] [INFO] Query marker FASTA was written to GCF_004368535.1_ASM436853v1_genomic.fna/markers.fasta
[2024-01-24 15:06:43,117] [INFO] Task started: Blastn
[2024-01-24 15:06:43,118] [INFO] Running command: blastn -query GCF_004368535.1_ASM436853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/reference_markers.fasta -out GCF_004368535.1_ASM436853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:43,958] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:43,966] [INFO] Selected 12 target genomes.
[2024-01-24 15:06:43,967] [INFO] Target genome list was writen to GCF_004368535.1_ASM436853v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:43,978] [INFO] Task started: fastANI
[2024-01-24 15:06:43,978] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdab3ef4-d70c-4b19-9131-8ceb93a48b0e/GCF_004368535.1_ASM436853v1_genomic.fna.gz --refList GCF_004368535.1_ASM436853v1_genomic.fna/target_genomes.txt --output GCF_004368535.1_ASM436853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:06:51,171] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:51,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:06:51,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:06:51,180] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:06:51,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:06:51,181] [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 haemolyticus	strain=ATCC 33390	GCA_004368535.1	726	726	type	True	100.0	604	604	95	conclusive
Haemophilus haemolyticus	strain=CCUG 12834	GCA_001679045.1	726	726	type	True	99.9929	599	604	95	conclusive
Haemophilus seminalis	strain=SZY H1	GCA_006384255.1	2582921	2582921	type	True	93.3717	486	604	95	below_threshold
Haemophilus influenzae	strain=FDAARGOS_1560	GCA_020736045.1	727	727	type	True	91.8299	470	604	95	below_threshold
Haemophilus influenzae	strain=NCTC8143	GCA_001457655.1	727	727	type	True	91.6881	479	604	95	below_threshold
Haemophilus aegyptius	strain=FDAARGOS_1478	GCA_019930905.1	197575	197575	type	True	91.5272	484	604	95	below_threshold
Haemophilus aegyptius	strain=NCTC8502	GCA_900475885.1	197575	197575	type	True	91.4594	486	604	95	below_threshold
Rodentibacter haemolyticus	strain=DSM 111151	GCA_015356115.1	2778911	2778911	type	True	79.515	323	604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:06:51,182] [INFO] DFAST Taxonomy check result was written to GCF_004368535.1_ASM436853v1_genomic.fna/tc_result.tsv
[2024-01-24 15:06:51,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:06:51,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:06:51,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/checkm_data
[2024-01-24 15:06:51,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:06:51,206] [INFO] Task started: CheckM
[2024-01-24 15:06:51,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004368535.1_ASM436853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004368535.1_ASM436853v1_genomic.fna/checkm_input GCF_004368535.1_ASM436853v1_genomic.fna/checkm_result
[2024-01-24 15:07:11,723] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:11,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:11,741] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:11,742] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:11,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004368535.1_ASM436853v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:11,743] [INFO] Task started: Blastn
[2024-01-24 15:07:11,743] [INFO] Running command: blastn -query GCF_004368535.1_ASM436853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e20ef7b-29bf-4b1e-acf2-192d6849d992/dqc_reference/reference_markers_gtdb.fasta -out GCF_004368535.1_ASM436853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:12,814] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:12,823] [INFO] Selected 13 target genomes.
[2024-01-24 15:07:12,824] [INFO] Target genome list was writen to GCF_004368535.1_ASM436853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:12,832] [INFO] Task started: fastANI
[2024-01-24 15:07:12,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdab3ef4-d70c-4b19-9131-8ceb93a48b0e/GCF_004368535.1_ASM436853v1_genomic.fna.gz --refList GCF_004368535.1_ASM436853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004368535.1_ASM436853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:07:19,415] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:19,432] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 15:07:19,432] [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_001679045.1	s__Haemophilus haemolyticus	99.9929	599	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.67	95.07	0.90	0.84	29	inconclusive
GCF_003352385.1	s__Haemophilus haemolyticus_I	95.0627	532	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.71	95.22	0.89	0.82	17	inconclusive
GCA_001752465.1	s__Haemophilus quentini	94.6215	533	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	99.94	99.85	0.97	0.94	5	-
GCF_003493605.1	s__Haemophilus haemolyticus_J	94.5764	505	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222025.1	s__Haemophilus haemolyticus_G	94.2575	524	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276515.1	s__Haemophilus sp001276515	94.1735	505	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	95.49	95.48	0.91	0.90	3	-
GCF_006384255.1	s__Haemophilus seminalis	93.3717	486	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.0	96.02	95.40	0.91	0.84	26	-
GCF_001457655.1	s__Haemophilus influenzae	91.7099	478	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.9609	97.88	97.07	0.94	0.87	511	-
GCF_004802395.1	s__Haemophilus influenzae_E	91.6894	485	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	96.8621	97.44	97.09	0.92	0.89	88	-
GCF_900475755.1	s__Haemophilus influenzae_D	91.39	486	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus	95.4263	96.90	95.46	0.91	0.81	69	-
GCA_018381425.1	s__Haemophilus_D parainfluenzae_O	83.3103	229	604	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_000210895.1	s__Haemophilus_D parainfluenzae_A	81.6795	334	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.08	95.08	0.92	0.92	2	-
GCF_003252795.1	s__Haemophilus_D parainfluenzae_K	81.5116	337	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D	95.0	95.28	95.03	0.93	0.88	19	-
--------------------------------------------------------------------------------
[2024-01-24 15:07:19,434] [INFO] GTDB search result was written to GCF_004368535.1_ASM436853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:07:19,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:07:19,438] [INFO] DFAST_QC result json was written to GCF_004368535.1_ASM436853v1_genomic.fna/dqc_result.json
[2024-01-24 15:07:19,438] [INFO] DFAST_QC completed!
[2024-01-24 15:07:19,438] [INFO] Total running time: 0h0m43s