[2024-01-25 17:35:50,795] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:50,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:50,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference
[2024-01-25 17:35:51,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:51,916] [INFO] Task started: Prodigal
[2024-01-25 17:35:51,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg91efa3d4-5f7b-4c78-b3dc-b69d5e1485c3/GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/cds.fna -a GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:57,426] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:57,426] [INFO] Task started: HMMsearch
[2024-01-25 17:35:57,426] [INFO] Running command: hmmsearch --tblout GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/reference_markers.hmm GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:57,638] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:57,639] [INFO] Found 6/6 markers.
[2024-01-25 17:35:57,661] [INFO] Query marker FASTA was written to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:35:57,662] [INFO] Task started: Blastn
[2024-01-25 17:35:57,662] [INFO] Running command: blastn -query GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/reference_markers.fasta -out GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:58,211] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:58,213] [INFO] Selected 16 target genomes.
[2024-01-25 17:35:58,213] [INFO] Target genome list was writen to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:35:58,219] [INFO] Task started: fastANI
[2024-01-25 17:35:58,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg91efa3d4-5f7b-4c78-b3dc-b69d5e1485c3/GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna.gz --refList GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:07,865] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:07,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:07,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:07,870] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:36:07,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:36:07,870] [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 faecalis	strain=DSM 20678	GCA_900115765.1	937334	937334	type	True	100.0	814	820	95	conclusive
Caldicoprobacter algeriensis	strain=TH7C1	GCA_023838525.1	699281	699281	type	True	91.6511	633	820	95	below_threshold
Caldicoprobacter guelmensis	strain=DSM 24605	GCA_016908415.1	1170224	1170224	type	True	82.5613	550	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:07,872] [INFO] DFAST Taxonomy check result was written to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:36:07,872] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:07,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:07,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/checkm_data
[2024-01-25 17:36:07,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:07,904] [INFO] Task started: CheckM
[2024-01-25 17:36:07,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/checkm_input GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:36:29,381] [INFO] Task succeeded: CheckM
[2024-01-25 17:36:29,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:36:29,400] [INFO] ===== Completeness check finished =====
[2024-01-25 17:36:29,400] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:36:29,401] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:36:29,401] [INFO] Task started: Blastn
[2024-01-25 17:36:29,401] [INFO] Running command: blastn -query GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7916491-ab46-4444-b7ff-f735cbe5f589/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:36:30,193] [INFO] Task succeeded: Blastn
[2024-01-25 17:36:30,197] [INFO] Selected 17 target genomes.
[2024-01-25 17:36:30,197] [INFO] Target genome list was writen to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:36:30,207] [INFO] Task started: fastANI
[2024-01-25 17:36:30,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg91efa3d4-5f7b-4c78-b3dc-b69d5e1485c3/GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna.gz --refList GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:39,504] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:39,507] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:39,508] [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
GCA_000526435.1	s__Caldicoprobacter oshimai	99.0007	789	820	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	98.85	98.71	0.91	0.85	3	conclusive
GCA_017577715.1	s__Caldicoprobacter sp017577715	84.5499	540	820	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908415.1	s__Caldicoprobacter guelmensis	82.5806	550	820	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Caldicoprobacterales;f__Caldicoprobacteraceae;g__Caldicoprobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:36:39,509] [INFO] GTDB search result was written to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:39,509] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:39,511] [INFO] DFAST_QC result json was written to GCF_900115765.1_IMG-taxon_2693429901_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:36:39,511] [INFO] DFAST_QC completed!
[2024-01-25 17:36:39,511] [INFO] Total running time: 0h0m49s