[2024-01-25 19:35:51,396] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,402] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,402] [INFO] DQC Reference Directory: /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference
[2024-01-25 19:35:52,542] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,544] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg839f53e5-7ccc-4450-b0b1-ab62eabc3f99/GCF_016025525.2_ASM1602552v2_genomic.fna.gz | prodigal -d GCF_016025525.2_ASM1602552v2_genomic.fna/cds.fna -a GCF_016025525.2_ASM1602552v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:59,227] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:59,227] [INFO] Task started: HMMsearch
[2024-01-25 19:35:59,227] [INFO] Running command: hmmsearch --tblout GCF_016025525.2_ASM1602552v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/reference_markers.hmm GCF_016025525.2_ASM1602552v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:59,460] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:59,461] [INFO] Found 6/6 markers.
[2024-01-25 19:35:59,485] [INFO] Query marker FASTA was written to GCF_016025525.2_ASM1602552v2_genomic.fna/markers.fasta
[2024-01-25 19:35:59,485] [INFO] Task started: Blastn
[2024-01-25 19:35:59,485] [INFO] Running command: blastn -query GCF_016025525.2_ASM1602552v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/reference_markers.fasta -out GCF_016025525.2_ASM1602552v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:00,304] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:00,311] [INFO] Selected 13 target genomes.
[2024-01-25 19:36:00,312] [INFO] Target genome list was writen to GCF_016025525.2_ASM1602552v2_genomic.fna/target_genomes.txt
[2024-01-25 19:36:00,319] [INFO] Task started: fastANI
[2024-01-25 19:36:00,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg839f53e5-7ccc-4450-b0b1-ab62eabc3f99/GCF_016025525.2_ASM1602552v2_genomic.fna.gz --refList GCF_016025525.2_ASM1602552v2_genomic.fna/target_genomes.txt --output GCF_016025525.2_ASM1602552v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:09,416] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:09,417] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:09,417] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:09,429] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:36:09,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:36:09,429] [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 longinqua	strain=NML02-A-017	GCA_001648355.1	1795827	1795827	type	True	91.8289	622	790	95	below_threshold
Eikenella halliae	strain=NML130454	GCA_001648475.1	1795832	1795832	type	True	86.3606	585	790	95	below_threshold
Eikenella corrodens	strain=ATCC 23834	GCA_000158615.1	539	539	type	True	85.6947	565	790	95	below_threshold
Eikenella corrodens	strain=NCTC10596	GCA_900187105.1	539	539	type	True	85.5881	559	790	95	below_threshold
Eikenella corrodens	strain=FDAARGOS_1474	GCA_019930845.1	539	539	type	True	85.4602	566	790	95	below_threshold
Eikenella exigua	strain=PXX	GCA_008805035.1	2528037	2528037	type	True	85.2268	521	790	95	below_threshold
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	79.4632	246	790	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.454	325	790	95	below_threshold
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	79.3479	261	790	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.2883	331	790	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.6958	224	790	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	78.5567	306	790	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.464	318	790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:09,431] [INFO] DFAST Taxonomy check result was written to GCF_016025525.2_ASM1602552v2_genomic.fna/tc_result.tsv
[2024-01-25 19:36:09,432] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:09,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:09,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/checkm_data
[2024-01-25 19:36:09,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:09,461] [INFO] Task started: CheckM
[2024-01-25 19:36:09,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016025525.2_ASM1602552v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016025525.2_ASM1602552v2_genomic.fna/checkm_input GCF_016025525.2_ASM1602552v2_genomic.fna/checkm_result
[2024-01-25 19:36:32,165] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:32,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:32,185] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:32,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:32,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016025525.2_ASM1602552v2_genomic.fna/markers.fasta)
[2024-01-25 19:36:32,186] [INFO] Task started: Blastn
[2024-01-25 19:36:32,186] [INFO] Running command: blastn -query GCF_016025525.2_ASM1602552v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgafb44550-74ef-450f-bf63-df869c7f53ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_016025525.2_ASM1602552v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:33,693] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:33,696] [INFO] Selected 6 target genomes.
[2024-01-25 19:36:33,696] [INFO] Target genome list was writen to GCF_016025525.2_ASM1602552v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:33,700] [INFO] Task started: fastANI
[2024-01-25 19:36:33,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg839f53e5-7ccc-4450-b0b1-ab62eabc3f99/GCF_016025525.2_ASM1602552v2_genomic.fna.gz --refList GCF_016025525.2_ASM1602552v2_genomic.fna/target_genomes_gtdb.txt --output GCF_016025525.2_ASM1602552v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:40,195] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:40,201] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:40,201] [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_016025525.2	s__Eikenella sp016025525	100.0	787	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001648355.1	s__Eikenella longinqua	91.8289	622	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648475.1	s__Eikenella halliae	86.3505	586	790	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	85.9796	586	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187105.1	s__Eikenella corrodens	85.5688	561	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.96	95.30	0.90	0.87	23	-
GCF_008805035.1	s__Eikenella exigua	85.2491	520	790	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.49	95.37	0.95	0.91	11	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:40,202] [INFO] GTDB search result was written to GCF_016025525.2_ASM1602552v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:40,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:40,206] [INFO] DFAST_QC result json was written to GCF_016025525.2_ASM1602552v2_genomic.fna/dqc_result.json
[2024-01-25 19:36:40,206] [INFO] DFAST_QC completed!
[2024-01-25 19:36:40,206] [INFO] Total running time: 0h0m49s