[2024-01-24 13:09:29,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,324] [INFO] DQC Reference Directory: /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference
[2024-01-24 13:09:30,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,560] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,560] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8e70fea-02cb-4451-956f-2b8ae836b735/GCF_004363775.1_ASM436377v1_genomic.fna.gz | prodigal -d GCF_004363775.1_ASM436377v1_genomic.fna/cds.fna -a GCF_004363775.1_ASM436377v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:37,761] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:37,762] [INFO] Task started: HMMsearch
[2024-01-24 13:09:37,762] [INFO] Running command: hmmsearch --tblout GCF_004363775.1_ASM436377v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/reference_markers.hmm GCF_004363775.1_ASM436377v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:38,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:38,033] [INFO] Found 6/6 markers.
[2024-01-24 13:09:38,055] [INFO] Query marker FASTA was written to GCF_004363775.1_ASM436377v1_genomic.fna/markers.fasta
[2024-01-24 13:09:38,055] [INFO] Task started: Blastn
[2024-01-24 13:09:38,056] [INFO] Running command: blastn -query GCF_004363775.1_ASM436377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/reference_markers.fasta -out GCF_004363775.1_ASM436377v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:38,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:38,745] [INFO] Selected 26 target genomes.
[2024-01-24 13:09:38,746] [INFO] Target genome list was writen to GCF_004363775.1_ASM436377v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:38,776] [INFO] Task started: fastANI
[2024-01-24 13:09:38,777] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e70fea-02cb-4451-956f-2b8ae836b735/GCF_004363775.1_ASM436377v1_genomic.fna.gz --refList GCF_004363775.1_ASM436377v1_genomic.fna/target_genomes.txt --output GCF_004363775.1_ASM436377v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:52,449] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:52,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:52,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:52,459] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:52,459] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:52,459] [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
Hydromonas duriensis	strain=DSM 102852	GCA_004363775.1	1527608	1527608	type	True	100.0	773	774	95	conclusive
Ephemeroptericola cinctiostellae	strain=F02	GCA_003339525.1	2268024	2268024	type	True	78.4026	249	774	95	below_threshold
Formosimonas limnophila	strain=KCTC 32501	GCA_014652675.1	1384487	1384487	type	True	78.2045	147	774	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:52,461] [INFO] DFAST Taxonomy check result was written to GCF_004363775.1_ASM436377v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:52,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:52,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:52,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/checkm_data
[2024-01-24 13:09:52,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:52,488] [INFO] Task started: CheckM
[2024-01-24 13:09:52,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363775.1_ASM436377v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363775.1_ASM436377v1_genomic.fna/checkm_input GCF_004363775.1_ASM436377v1_genomic.fna/checkm_result
[2024-01-24 13:10:21,347] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:21,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:21,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:21,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:21,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363775.1_ASM436377v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:21,374] [INFO] Task started: Blastn
[2024-01-24 13:10:21,374] [INFO] Running command: blastn -query GCF_004363775.1_ASM436377v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga147db0d-22dd-4b5c-b1ed-b21dc336c004/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363775.1_ASM436377v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:22,516] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:22,520] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:22,520] [INFO] Target genome list was writen to GCF_004363775.1_ASM436377v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:22,549] [INFO] Task started: fastANI
[2024-01-24 13:10:22,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8e70fea-02cb-4451-956f-2b8ae836b735/GCF_004363775.1_ASM436377v1_genomic.fna.gz --refList GCF_004363775.1_ASM436377v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363775.1_ASM436377v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,161] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,173] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,173] [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_004363775.1	s__Hydromonas duriensis	100.0	773	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003339525.1	s__Hydromonas cinctiostellae	78.4186	248	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652675.1	s__Formosimonas limnophila	78.1901	147	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Formosimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495165.1	s__Formosimonas sp017495165	77.0609	129	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Formosimonas	95.0	99.98	99.98	0.98	0.98	4	-
GCA_018261955.1	s__CTSOIL-112 sp018261955	76.9569	93	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CTSOIL-112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017986195.1	s__CTSOIL-112 sp017986195	76.7034	62	774	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CTSOIL-112	95.0	98.81	98.81	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,175] [INFO] GTDB search result was written to GCF_004363775.1_ASM436377v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,175] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,182] [INFO] DFAST_QC result json was written to GCF_004363775.1_ASM436377v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,182] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,182] [INFO] Total running time: 0h1m5s