[2024-01-24 12:31:04,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:04,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:04,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference
[2024-01-24 12:31:05,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:05,792] [INFO] Task started: Prodigal
[2024-01-24 12:31:05,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg546007b9-c5c8-41ab-bb50-6e291bf4e309/GCF_016604485.1_ASM1660448v1_genomic.fna.gz | prodigal -d GCF_016604485.1_ASM1660448v1_genomic.fna/cds.fna -a GCF_016604485.1_ASM1660448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:11,002] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:11,002] [INFO] Task started: HMMsearch
[2024-01-24 12:31:11,003] [INFO] Running command: hmmsearch --tblout GCF_016604485.1_ASM1660448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/reference_markers.hmm GCF_016604485.1_ASM1660448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:11,263] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:11,265] [INFO] Found 6/6 markers.
[2024-01-24 12:31:11,292] [INFO] Query marker FASTA was written to GCF_016604485.1_ASM1660448v1_genomic.fna/markers.fasta
[2024-01-24 12:31:11,293] [INFO] Task started: Blastn
[2024-01-24 12:31:11,293] [INFO] Running command: blastn -query GCF_016604485.1_ASM1660448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/reference_markers.fasta -out GCF_016604485.1_ASM1660448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:11,859] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:11,863] [INFO] Selected 24 target genomes.
[2024-01-24 12:31:11,864] [INFO] Target genome list was writen to GCF_016604485.1_ASM1660448v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:11,881] [INFO] Task started: fastANI
[2024-01-24 12:31:11,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg546007b9-c5c8-41ab-bb50-6e291bf4e309/GCF_016604485.1_ASM1660448v1_genomic.fna.gz --refList GCF_016604485.1_ASM1660448v1_genomic.fna/target_genomes.txt --output GCF_016604485.1_ASM1660448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:24,819] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:24,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:24,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:24,835] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:24,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:24,836] [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
Fangia hongkongensis	strain=FSC776	GCA_016604485.1	270495	270495	type	True	100.0	620	632	95	conclusive
Fangia hongkongensis	strain=DSM 21703	GCA_000379445.1	270495	270495	type	True	99.9993	632	632	95	conclusive
Cysteiniphilum litorale	strain=DSM 101832	GCA_003428165.1	2056700	2056700	type	True	78.0193	92	632	95	below_threshold
Cysteiniphilum litorale	strain=CGMCC 1.15758	GCA_014643575.1	2056700	2056700	type	True	77.9194	92	632	95	below_threshold
Fastidiosibacter lacustris	strain=NBRC 112274	GCA_003428155.1	2056695	2056695	type	True	77.3277	72	632	95	below_threshold
Cysteiniphilum halobium	strain=SYSU SYW-6	GCA_003574425.1	2219059	2219059	type	True	77.3185	85	632	95	below_threshold
Cysteiniphilum marinum	strain=19X3-30	GCA_014857925.1	2774191	2774191	type	True	77.0056	90	632	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:24,838] [INFO] DFAST Taxonomy check result was written to GCF_016604485.1_ASM1660448v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:24,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:24,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:24,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/checkm_data
[2024-01-24 12:31:24,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:24,869] [INFO] Task started: CheckM
[2024-01-24 12:31:24,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016604485.1_ASM1660448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016604485.1_ASM1660448v1_genomic.fna/checkm_input GCF_016604485.1_ASM1660448v1_genomic.fna/checkm_result
[2024-01-24 12:31:47,924] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:47,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:47,949] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:47,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:47,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016604485.1_ASM1660448v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:47,950] [INFO] Task started: Blastn
[2024-01-24 12:31:47,950] [INFO] Running command: blastn -query GCF_016604485.1_ASM1660448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e07851-fde5-4491-9bee-928a84fa3a6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016604485.1_ASM1660448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:48,797] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:48,802] [INFO] Selected 31 target genomes.
[2024-01-24 12:31:48,802] [INFO] Target genome list was writen to GCF_016604485.1_ASM1660448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:48,877] [INFO] Task started: fastANI
[2024-01-24 12:31:48,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg546007b9-c5c8-41ab-bb50-6e291bf4e309/GCF_016604485.1_ASM1660448v1_genomic.fna.gz --refList GCF_016604485.1_ASM1660448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016604485.1_ASM1660448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:02,590] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:02,601] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:02,602] [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_000379445.1	s__Fangia hongkongensis	99.9993	632	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Fangia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003428165.1	s__Cysteiniphilum litorale	77.9833	93	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.98	99.97	0.98	0.97	3	-
GCF_003574485.1	s__Facilibium subflavum	77.6406	83	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Facilibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008711525.1	s__Cysteiniphilum sp008711525	77.5583	74	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428155.1	s__Fastidiosibacter lacustris	77.3277	72	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Fastidiosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574425.1	s__Cysteiniphilum halobium	77.3185	85	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014857925.1	s__Cysteiniphilum marinum	77.0056	90	632	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.88	99.82	0.94	0.93	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:02,603] [INFO] GTDB search result was written to GCF_016604485.1_ASM1660448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:02,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:02,606] [INFO] DFAST_QC result json was written to GCF_016604485.1_ASM1660448v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:02,606] [INFO] DFAST_QC completed!
[2024-01-24 12:32:02,607] [INFO] Total running time: 0h0m58s