[2024-01-24 12:40:04,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:04,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:04,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference
[2024-01-24 12:40:06,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:06,241] [INFO] Task started: Prodigal
[2024-01-24 12:40:06,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg75d11f67-bfbb-4a2d-bb4e-dc63a345fcb6/GCF_019930845.1_ASM1993084v1_genomic.fna.gz | prodigal -d GCF_019930845.1_ASM1993084v1_genomic.fna/cds.fna -a GCF_019930845.1_ASM1993084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:13,335] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:13,335] [INFO] Task started: HMMsearch
[2024-01-24 12:40:13,335] [INFO] Running command: hmmsearch --tblout GCF_019930845.1_ASM1993084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/reference_markers.hmm GCF_019930845.1_ASM1993084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:13,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:13,601] [INFO] Found 6/6 markers.
[2024-01-24 12:40:13,628] [INFO] Query marker FASTA was written to GCF_019930845.1_ASM1993084v1_genomic.fna/markers.fasta
[2024-01-24 12:40:13,629] [INFO] Task started: Blastn
[2024-01-24 12:40:13,629] [INFO] Running command: blastn -query GCF_019930845.1_ASM1993084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/reference_markers.fasta -out GCF_019930845.1_ASM1993084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:14,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:14,544] [INFO] Selected 11 target genomes.
[2024-01-24 12:40:14,544] [INFO] Target genome list was writen to GCF_019930845.1_ASM1993084v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:14,552] [INFO] Task started: fastANI
[2024-01-24 12:40:14,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg75d11f67-bfbb-4a2d-bb4e-dc63a345fcb6/GCF_019930845.1_ASM1993084v1_genomic.fna.gz --refList GCF_019930845.1_ASM1993084v1_genomic.fna/target_genomes.txt --output GCF_019930845.1_ASM1993084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:25,211] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:25,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:25,212] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:25,228] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:25,229] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:25,229] [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 corrodens	strain=FDAARGOS_1474	GCA_019930845.1	539	539	type	True	100.0	727	730	95	conclusive
Eikenella corrodens	strain=NCTC10596	GCA_900187105.1	539	539	type	True	99.9997	727	730	95	conclusive
Eikenella corrodens	strain=ATCC 23834	GCA_000158615.1	539	539	type	True	99.9159	714	730	95	conclusive
Eikenella halliae	strain=NML130454	GCA_001648475.1	1795832	1795832	type	True	93.0889	615	730	95	below_threshold
Eikenella exigua	strain=PXX	GCA_008805035.1	2528037	2528037	type	True	92.057	562	730	95	below_threshold
Eikenella longinqua	strain=NML02-A-017	GCA_001648355.1	1795827	1795827	type	True	86.0141	560	730	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.7278	276	730	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.3675	313	730	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.2647	231	730	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.2471	299	730	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.1983	259	730	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:25,230] [INFO] DFAST Taxonomy check result was written to GCF_019930845.1_ASM1993084v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:25,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:25,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:25,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/checkm_data
[2024-01-24 12:40:25,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:25,261] [INFO] Task started: CheckM
[2024-01-24 12:40:25,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930845.1_ASM1993084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930845.1_ASM1993084v1_genomic.fna/checkm_input GCF_019930845.1_ASM1993084v1_genomic.fna/checkm_result
[2024-01-24 12:40:51,002] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:51,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:51,020] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:51,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:51,021] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930845.1_ASM1993084v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:51,021] [INFO] Task started: Blastn
[2024-01-24 12:40:51,021] [INFO] Running command: blastn -query GCF_019930845.1_ASM1993084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg052a4f06-c3f6-4e17-8343-b713a75b8ad5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930845.1_ASM1993084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:52,476] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:52,481] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:52,481] [INFO] Target genome list was writen to GCF_019930845.1_ASM1993084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:52,486] [INFO] Task started: fastANI
[2024-01-24 12:40:52,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg75d11f67-bfbb-4a2d-bb4e-dc63a345fcb6/GCF_019930845.1_ASM1993084v1_genomic.fna.gz --refList GCF_019930845.1_ASM1993084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930845.1_ASM1993084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:00,443] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:00,457] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:00,457] [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_900187105.1	s__Eikenella corrodens	99.9997	727	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	conclusive
GCF_001648475.1	s__Eikenella halliae	93.0889	615	730	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	92.8531	621	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008805035.1	s__Eikenella exigua	92.0592	562	730	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.49	95.37	0.95	0.91	11	-
GCF_001648355.1	s__Eikenella longinqua	86.1215	552	730	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	85.4547	574	730	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	81.3704	264	730	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 12:41:00,459] [INFO] GTDB search result was written to GCF_019930845.1_ASM1993084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:00,460] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:00,464] [INFO] DFAST_QC result json was written to GCF_019930845.1_ASM1993084v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:00,464] [INFO] DFAST_QC completed!
[2024-01-24 12:41:00,465] [INFO] Total running time: 0h0m56s