[2024-01-24 13:28:01,679] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,681] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference
[2024-01-24 13:28:02,923] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,924] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,924] [INFO] Running command: gunzip -c /var/lib/cwl/stgf32e1a73-0b3f-4082-ae3d-dfca405a02a5/GCF_000378405.1_ASM37840v1_genomic.fna.gz | prodigal -d GCF_000378405.1_ASM37840v1_genomic.fna/cds.fna -a GCF_000378405.1_ASM37840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:11,444] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:11,444] [INFO] Task started: HMMsearch
[2024-01-24 13:28:11,444] [INFO] Running command: hmmsearch --tblout GCF_000378405.1_ASM37840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/reference_markers.hmm GCF_000378405.1_ASM37840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:11,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:11,714] [INFO] Found 6/6 markers.
[2024-01-24 13:28:11,748] [INFO] Query marker FASTA was written to GCF_000378405.1_ASM37840v1_genomic.fna/markers.fasta
[2024-01-24 13:28:11,748] [INFO] Task started: Blastn
[2024-01-24 13:28:11,748] [INFO] Running command: blastn -query GCF_000378405.1_ASM37840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/reference_markers.fasta -out GCF_000378405.1_ASM37840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:12,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:12,418] [INFO] Selected 27 target genomes.
[2024-01-24 13:28:12,419] [INFO] Target genome list was writen to GCF_000378405.1_ASM37840v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:12,430] [INFO] Task started: fastANI
[2024-01-24 13:28:12,431] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32e1a73-0b3f-4082-ae3d-dfca405a02a5/GCF_000378405.1_ASM37840v1_genomic.fna.gz --refList GCF_000378405.1_ASM37840v1_genomic.fna/target_genomes.txt --output GCF_000378405.1_ASM37840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:29,087] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:29,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:29,097] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:29,097] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:29,097] [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
Succinimonas amylolytica	strain=DSM 2873	GCA_000378405.1	83769	83769	type	True	99.9516	1216	1308	95	conclusive
Ruminobacter amylophilus	strain=DSM 1361	GCA_900115655.1	867	867	type	True	81.3273	117	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,099] [INFO] DFAST Taxonomy check result was written to GCF_000378405.1_ASM37840v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:29,100] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:29,100] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:29,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/checkm_data
[2024-01-24 13:28:29,102] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:29,143] [INFO] Task started: CheckM
[2024-01-24 13:28:29,143] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000378405.1_ASM37840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000378405.1_ASM37840v1_genomic.fna/checkm_input GCF_000378405.1_ASM37840v1_genomic.fna/checkm_result
[2024-01-24 13:28:59,118] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:59,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,148] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:59,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:59,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000378405.1_ASM37840v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:59,149] [INFO] Task started: Blastn
[2024-01-24 13:28:59,149] [INFO] Running command: blastn -query GCF_000378405.1_ASM37840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fa82314-d035-4e3a-8040-ba8e196665cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000378405.1_ASM37840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:00,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:00,151] [INFO] Selected 19 target genomes.
[2024-01-24 13:29:00,151] [INFO] Target genome list was writen to GCF_000378405.1_ASM37840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:00,172] [INFO] Task started: fastANI
[2024-01-24 13:29:00,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgf32e1a73-0b3f-4082-ae3d-dfca405a02a5/GCF_000378405.1_ASM37840v1_genomic.fna.gz --refList GCF_000378405.1_ASM37840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000378405.1_ASM37840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:12,579] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:12,585] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:12,586] [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_000378405.1	s__Succinimonas amylolytica	99.9516	1216	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902776415.1	s__Succinimonas sp902776415	84.0764	710	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372325.1	s__Succinimonas sp002372325	80.3368	491	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinimonas	95.0	97.12	96.26	0.77	0.74	3	-
GCA_902764345.1	s__Ruminobacter sp002309455	78.7642	86	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Ruminobacter	95.0	98.59	98.46	0.92	0.91	3	-
GCA_017940385.1	s__Ruminobacter sp017940385	78.0715	85	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Ruminobacter	95.0	98.94	98.94	0.96	0.96	2	-
GCA_900315145.1	s__Ruminobacter sp900315145	77.9	81	1308	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Ruminobacter	95.0	99.04	98.60	0.89	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,587] [INFO] GTDB search result was written to GCF_000378405.1_ASM37840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:12,588] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:12,590] [INFO] DFAST_QC result json was written to GCF_000378405.1_ASM37840v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:12,590] [INFO] DFAST_QC completed!
[2024-01-24 13:29:12,590] [INFO] Total running time: 0h1m11s