[2024-01-25 17:39:20,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:20,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:20,658] [INFO] DQC Reference Directory: /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference
[2024-01-25 17:39:21,848] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:21,849] [INFO] Task started: Prodigal
[2024-01-25 17:39:21,849] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8ac5604-7d39-4a39-9b94-1e70cc7af750/GCF_002803295.2_ASM280329v2_genomic.fna.gz | prodigal -d GCF_002803295.2_ASM280329v2_genomic.fna/cds.fna -a GCF_002803295.2_ASM280329v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:24,557] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:24,557] [INFO] Task started: HMMsearch
[2024-01-25 17:39:24,558] [INFO] Running command: hmmsearch --tblout GCF_002803295.2_ASM280329v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/reference_markers.hmm GCF_002803295.2_ASM280329v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:24,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:24,746] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8ac5604-7d39-4a39-9b94-1e70cc7af750/GCF_002803295.2_ASM280329v2_genomic.fna.gz]
[2024-01-25 17:39:24,760] [INFO] Query marker FASTA was written to GCF_002803295.2_ASM280329v2_genomic.fna/markers.fasta
[2024-01-25 17:39:24,760] [INFO] Task started: Blastn
[2024-01-25 17:39:24,761] [INFO] Running command: blastn -query GCF_002803295.2_ASM280329v2_genomic.fna/markers.fasta -db /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/reference_markers.fasta -out GCF_002803295.2_ASM280329v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:25,346] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:25,349] [INFO] Selected 20 target genomes.
[2024-01-25 17:39:25,349] [INFO] Target genome list was writen to GCF_002803295.2_ASM280329v2_genomic.fna/target_genomes.txt
[2024-01-25 17:39:25,374] [INFO] Task started: fastANI
[2024-01-25 17:39:25,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ac5604-7d39-4a39-9b94-1e70cc7af750/GCF_002803295.2_ASM280329v2_genomic.fna.gz --refList GCF_002803295.2_ASM280329v2_genomic.fna/target_genomes.txt --output GCF_002803295.2_ASM280329v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:35,428] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:35,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:35,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:35,445] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:35,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:35,445] [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
Caedibacter taeniospiralis	strain=51K	GCA_002803295.2	28907	28907	type	True	100.0	430	432	95	conclusive
Fastidiosibacter lacustris	strain=NBRC 112274	GCA_003428155.1	2056695	2056695	type	True	77.9348	91	432	95	below_threshold
Cysteiniphilum litorale	strain=CGMCC 1.15758	GCA_014643575.1	2056700	2056700	type	True	77.6658	134	432	95	below_threshold
Cysteiniphilum litorale	strain=DSM 101832	GCA_003428165.1	2056700	2056700	type	True	77.5323	130	432	95	below_threshold
Cysteiniphilum halobium	strain=SYSU SYW-6	GCA_003574425.1	2219059	2219059	type	True	77.48	121	432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:35,447] [INFO] DFAST Taxonomy check result was written to GCF_002803295.2_ASM280329v2_genomic.fna/tc_result.tsv
[2024-01-25 17:39:35,447] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:35,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:35,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/checkm_data
[2024-01-25 17:39:35,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:35,464] [INFO] Task started: CheckM
[2024-01-25 17:39:35,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002803295.2_ASM280329v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002803295.2_ASM280329v2_genomic.fna/checkm_input GCF_002803295.2_ASM280329v2_genomic.fna/checkm_result
[2024-01-25 17:39:50,263] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:50,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:50,288] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:50,288] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:50,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002803295.2_ASM280329v2_genomic.fna/markers.fasta)
[2024-01-25 17:39:50,288] [INFO] Task started: Blastn
[2024-01-25 17:39:50,288] [INFO] Running command: blastn -query GCF_002803295.2_ASM280329v2_genomic.fna/markers.fasta -db /var/lib/cwl/stged933049-ec29-4704-ab4e-5444f1bca4ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_002803295.2_ASM280329v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:51,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:51,241] [INFO] Selected 17 target genomes.
[2024-01-25 17:39:51,241] [INFO] Target genome list was writen to GCF_002803295.2_ASM280329v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:51,274] [INFO] Task started: fastANI
[2024-01-25 17:39:51,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8ac5604-7d39-4a39-9b94-1e70cc7af750/GCF_002803295.2_ASM280329v2_genomic.fna.gz --refList GCF_002803295.2_ASM280329v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002803295.2_ASM280329v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:59,395] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:59,400] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:59,400] [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_002803295.2	s__Caedibacter taeniospiralis	100.0	430	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Caedibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003428155.1	s__Fastidiosibacter lacustris	77.9348	91	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Fastidiosibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014857925.1	s__Cysteiniphilum marinum	77.6708	130	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.88	99.82	0.94	0.93	7	-
GCF_003428165.1	s__Cysteiniphilum litorale	77.5028	133	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.98	99.97	0.98	0.97	3	-
GCF_008711525.1	s__Cysteiniphilum sp008711525	77.4994	125	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574425.1	s__Cysteiniphilum halobium	77.4557	122	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:59,401] [INFO] GTDB search result was written to GCF_002803295.2_ASM280329v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:59,402] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:59,404] [INFO] DFAST_QC result json was written to GCF_002803295.2_ASM280329v2_genomic.fna/dqc_result.json
[2024-01-25 17:39:59,404] [INFO] DFAST_QC completed!
[2024-01-25 17:39:59,404] [INFO] Total running time: 0h0m39s