[2024-01-25 18:03:35,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:35,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:35,498] [INFO] DQC Reference Directory: /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference
[2024-01-25 18:03:36,622] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:36,622] [INFO] Task started: Prodigal
[2024-01-25 18:03:36,623] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7f079c1-d3ee-464c-b1fd-2a18c8f795f6/GCF_016908415.1_ASM1690841v1_genomic.fna.gz | prodigal -d GCF_016908415.1_ASM1690841v1_genomic.fna/cds.fna -a GCF_016908415.1_ASM1690841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:41,883] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:41,883] [INFO] Task started: HMMsearch
[2024-01-25 18:03:41,883] [INFO] Running command: hmmsearch --tblout GCF_016908415.1_ASM1690841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/reference_markers.hmm GCF_016908415.1_ASM1690841v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:42,113] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:42,114] [INFO] Found 6/6 markers.
[2024-01-25 18:03:42,147] [INFO] Query marker FASTA was written to GCF_016908415.1_ASM1690841v1_genomic.fna/markers.fasta
[2024-01-25 18:03:42,147] [INFO] Task started: Blastn
[2024-01-25 18:03:42,147] [INFO] Running command: blastn -query GCF_016908415.1_ASM1690841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/reference_markers.fasta -out GCF_016908415.1_ASM1690841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:42,681] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:42,692] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:42,693] [INFO] Target genome list was writen to GCF_016908415.1_ASM1690841v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:42,714] [INFO] Task started: fastANI
[2024-01-25 18:03:42,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f079c1-d3ee-464c-b1fd-2a18c8f795f6/GCF_016908415.1_ASM1690841v1_genomic.fna.gz --refList GCF_016908415.1_ASM1690841v1_genomic.fna/target_genomes.txt --output GCF_016908415.1_ASM1690841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:49,976] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:49,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:49,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:49,982] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:49,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:49,983] [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
Caldicoprobacter guelmensis	strain=DSM 24605	GCA_016908415.1	1170224	1170224	type	True	100.0	788	790	95	conclusive
Caldicoprobacter algeriensis	strain=TH7C1	GCA_023838525.1	699281	699281	type	True	83.6074	590	790	95	below_threshold
Caldicoprobacter faecalis	strain=DSM 20678	GCA_900115765.1	937334	937334	type	True	82.901	530	790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:49,992] [INFO] DFAST Taxonomy check result was written to GCF_016908415.1_ASM1690841v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:49,993] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:49,994] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:49,994] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/checkm_data
[2024-01-25 18:03:49,995] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:50,032] [INFO] Task started: CheckM
[2024-01-25 18:03:50,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908415.1_ASM1690841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908415.1_ASM1690841v1_genomic.fna/checkm_input GCF_016908415.1_ASM1690841v1_genomic.fna/checkm_result
[2024-01-25 18:04:10,745] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:10,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:10,766] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:10,766] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:10,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908415.1_ASM1690841v1_genomic.fna/markers.fasta)
[2024-01-25 18:04:10,767] [INFO] Task started: Blastn
[2024-01-25 18:04:10,767] [INFO] Running command: blastn -query GCF_016908415.1_ASM1690841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc92ba5f0-fdb7-4071-b4c8-3964b219e047/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908415.1_ASM1690841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:11,511] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:11,514] [INFO] Selected 16 target genomes.
[2024-01-25 18:04:11,514] [INFO] Target genome list was writen to GCF_016908415.1_ASM1690841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:11,551] [INFO] Task started: fastANI
[2024-01-25 18:04:11,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7f079c1-d3ee-464c-b1fd-2a18c8f795f6/GCF_016908415.1_ASM1690841v1_genomic.fna.gz --refList GCF_016908415.1_ASM1690841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908415.1_ASM1690841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:18,786] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:18,790] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:18,791] [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_016908415.1	s__Caldicoprobacter guelmensis	100.0	788	790	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000526435.1	s__Caldicoprobacter oshimai	82.8357	544	790	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	98.85	98.71	0.91	0.85	3	-
GCA_017577715.1	s__Caldicoprobacter sp017577715	80.1573	412	790	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385885.1	s__DTU074 sp002385885	76.6217	53	790	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__DTU074	95.0	99.88	99.84	0.86	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:18,792] [INFO] GTDB search result was written to GCF_016908415.1_ASM1690841v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:18,792] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:18,794] [INFO] DFAST_QC result json was written to GCF_016908415.1_ASM1690841v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:18,794] [INFO] DFAST_QC completed!
[2024-01-25 18:04:18,794] [INFO] Total running time: 0h0m43s