[2024-01-24 13:12:53,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:53,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:53,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference
[2024-01-24 13:12:54,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:54,318] [INFO] Task started: Prodigal
[2024-01-24 13:12:54,319] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcbd6364-ce60-48ae-b485-c8bd43a5a8d1/GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/cds.fna -a GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:02,213] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:02,213] [INFO] Task started: HMMsearch
[2024-01-24 13:13:02,213] [INFO] Running command: hmmsearch --tblout GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/reference_markers.hmm GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:02,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:02,532] [INFO] Found 6/6 markers.
[2024-01-24 13:13:02,558] [INFO] Query marker FASTA was written to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:02,559] [INFO] Task started: Blastn
[2024-01-24 13:13:02,559] [INFO] Running command: blastn -query GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/reference_markers.fasta -out GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:03,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:03,169] [INFO] Selected 22 target genomes.
[2024-01-24 13:13:03,169] [INFO] Target genome list was writen to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:03,201] [INFO] Task started: fastANI
[2024-01-24 13:13:03,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcbd6364-ce60-48ae-b485-c8bd43a5a8d1/GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna.gz --refList GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:16,452] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:16,453] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:16,453] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:16,459] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:16,459] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:16,459] [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
Sporomusa sphaeroides	strain=DSM 2875	GCA_001941975.1	47679	47679	type	True	76.0712	50	926	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	75.7831	59	926	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:16,462] [INFO] DFAST Taxonomy check result was written to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:16,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:16,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:16,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/checkm_data
[2024-01-24 13:13:16,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:16,496] [INFO] Task started: CheckM
[2024-01-24 13:13:16,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/checkm_input GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:13:45,226] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:45,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:45,247] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:45,247] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:45,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:13:45,248] [INFO] Task started: Blastn
[2024-01-24 13:13:45,248] [INFO] Running command: blastn -query GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8297b72-fe44-4f60-b3cc-60b8744523f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:46,102] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:46,106] [INFO] Selected 17 target genomes.
[2024-01-24 13:13:46,107] [INFO] Target genome list was writen to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:46,124] [INFO] Task started: fastANI
[2024-01-24 13:13:46,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcbd6364-ce60-48ae-b485-c8bd43a5a8d1/GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna.gz --refList GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:54,409] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:54,421] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:54,422] [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_900102435.1	s__Sporolituus thermophilus	100.0	920	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Sporolituus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000169155.1	s__Thermosinus carboxydivorans	90.7024	733	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Thermosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482545.1	s__UBA7701 sp002482545	76.4833	82	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UBA7701;g__UBA7701	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941975.1	s__Sporomusa sphaeroides	76.0712	50	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	98.27	97.38	0.92	0.86	4	-
GCF_900476375.1	s__Lucifera butyrica	76.0692	68	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UPPP01;g__Lucifera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542835.1	s__Anaerosporomusa sp900542835	75.7921	51	926	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales_A;f__Acetonemaceae;g__Anaerosporomusa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,426] [INFO] GTDB search result was written to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:54,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:54,430] [INFO] DFAST_QC result json was written to GCF_900102435.1_IMG-taxon_2599185233_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:13:54,430] [INFO] DFAST_QC completed!
[2024-01-24 13:13:54,430] [INFO] Total running time: 0h1m1s