[2024-01-24 15:26:55,145] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,147] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference
[2024-01-24 15:26:56,576] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,577] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,577] [INFO] Running command: gunzip -c /var/lib/cwl/stg36688cfe-01b9-44ea-94e8-bc1f964d3c73/GCF_008805035.1_ASM880503v1_genomic.fna.gz | prodigal -d GCF_008805035.1_ASM880503v1_genomic.fna/cds.fna -a GCF_008805035.1_ASM880503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:03,220] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:03,220] [INFO] Task started: HMMsearch
[2024-01-24 15:27:03,220] [INFO] Running command: hmmsearch --tblout GCF_008805035.1_ASM880503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/reference_markers.hmm GCF_008805035.1_ASM880503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:03,499] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:03,500] [INFO] Found 6/6 markers.
[2024-01-24 15:27:03,522] [INFO] Query marker FASTA was written to GCF_008805035.1_ASM880503v1_genomic.fna/markers.fasta
[2024-01-24 15:27:03,523] [INFO] Task started: Blastn
[2024-01-24 15:27:03,523] [INFO] Running command: blastn -query GCF_008805035.1_ASM880503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/reference_markers.fasta -out GCF_008805035.1_ASM880503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:04,365] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:04,368] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:04,369] [INFO] Target genome list was writen to GCF_008805035.1_ASM880503v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:04,373] [INFO] Task started: fastANI
[2024-01-24 15:27:04,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg36688cfe-01b9-44ea-94e8-bc1f964d3c73/GCF_008805035.1_ASM880503v1_genomic.fna.gz --refList GCF_008805035.1_ASM880503v1_genomic.fna/target_genomes.txt --output GCF_008805035.1_ASM880503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:12,268] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:12,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:12,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:12,279] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:12,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:12,280] [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
Eikenella exigua	strain=PXX	GCA_008805035.1	2528037	2528037	type	True	100.0	661	664	95	conclusive
Eikenella corrodens	strain=NCTC10596	GCA_900187105.1	539	539	type	True	92.2507	547	664	95	below_threshold
Eikenella corrodens	strain=FDAARGOS_1474	GCA_019930845.1	539	539	type	True	92.2463	546	664	95	below_threshold
Eikenella corrodens	strain=ATCC 23834	GCA_000158615.1	539	539	type	True	92.1693	541	664	95	below_threshold
Eikenella halliae	strain=NML130454	GCA_001648475.1	1795832	1795832	type	True	91.4389	576	664	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.1737	219	664	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	80.0084	205	664	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.5193	242	664	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.3366	241	664	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.1458	193	664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:12,281] [INFO] DFAST Taxonomy check result was written to GCF_008805035.1_ASM880503v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:12,282] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:12,282] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:12,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/checkm_data
[2024-01-24 15:27:12,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:12,306] [INFO] Task started: CheckM
[2024-01-24 15:27:12,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008805035.1_ASM880503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008805035.1_ASM880503v1_genomic.fna/checkm_input GCF_008805035.1_ASM880503v1_genomic.fna/checkm_result
[2024-01-24 15:27:36,753] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:36,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,772] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:36,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:36,772] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008805035.1_ASM880503v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:36,773] [INFO] Task started: Blastn
[2024-01-24 15:27:36,773] [INFO] Running command: blastn -query GCF_008805035.1_ASM880503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29edeff6-f8df-48ed-85f1-0869b891eff8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008805035.1_ASM880503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:38,314] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:38,318] [INFO] Selected 7 target genomes.
[2024-01-24 15:27:38,318] [INFO] Target genome list was writen to GCF_008805035.1_ASM880503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:38,324] [INFO] Task started: fastANI
[2024-01-24 15:27:38,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg36688cfe-01b9-44ea-94e8-bc1f964d3c73/GCF_008805035.1_ASM880503v1_genomic.fna.gz --refList GCF_008805035.1_ASM880503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008805035.1_ASM880503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:44,669] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:44,676] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:44,677] [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_008805035.1	s__Eikenella exigua	100.0	662	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.49	95.37	0.95	0.91	11	conclusive
GCF_900187105.1	s__Eikenella corrodens	92.2256	544	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	-
GCF_001648475.1	s__Eikenella halliae	91.4404	576	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	91.3265	552	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648355.1	s__Eikenella longinqua	85.8014	505	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025525.2	s__Eikenella sp016025525	85.5409	513	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190695.1	s__Kingella_A denitrificans	80.8849	206	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:44,678] [INFO] GTDB search result was written to GCF_008805035.1_ASM880503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:44,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:44,682] [INFO] DFAST_QC result json was written to GCF_008805035.1_ASM880503v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:44,682] [INFO] DFAST_QC completed!
[2024-01-24 15:27:44,683] [INFO] Total running time: 0h0m50s