[2024-01-24 10:47:11,672] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference
[2024-01-24 10:47:16,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,945] [INFO] Running command: gunzip -c /var/lib/cwl/stgf81bf4da-39d5-4090-8f2e-d3fdc5e366fb/GCF_018141445.1_ASM1814144v1_genomic.fna.gz | prodigal -d GCF_018141445.1_ASM1814144v1_genomic.fna/cds.fna -a GCF_018141445.1_ASM1814144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,518] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,518] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,518] [INFO] Running command: hmmsearch --tblout GCF_018141445.1_ASM1814144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/reference_markers.hmm GCF_018141445.1_ASM1814144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:33,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:33,873] [INFO] Found 6/6 markers.
[2024-01-24 10:47:33,935] [INFO] Query marker FASTA was written to GCF_018141445.1_ASM1814144v1_genomic.fna/markers.fasta
[2024-01-24 10:47:33,936] [INFO] Task started: Blastn
[2024-01-24 10:47:33,936] [INFO] Running command: blastn -query GCF_018141445.1_ASM1814144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/reference_markers.fasta -out GCF_018141445.1_ASM1814144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:34,570] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:34,575] [INFO] Selected 25 target genomes.
[2024-01-24 10:47:34,576] [INFO] Target genome list was writen to GCF_018141445.1_ASM1814144v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:42,186] [INFO] Task started: fastANI
[2024-01-24 10:47:42,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81bf4da-39d5-4090-8f2e-d3fdc5e366fb/GCF_018141445.1_ASM1814144v1_genomic.fna.gz --refList GCF_018141445.1_ASM1814144v1_genomic.fna/target_genomes.txt --output GCF_018141445.1_ASM1814144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:59,786] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:59,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:59,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:59,798] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:59,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:59,799] [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
Vallitalea pronyensis	strain=FatNI3	GCA_018141445.1	1348613	1348613	type	True	100.0	2108	2108	95	conclusive
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	78.2658	282	2108	95	below_threshold
Natranaerovirga hydrolytica	strain=DSM 24176	GCA_004339095.1	680378	680378	type	True	76.5665	57	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:59,801] [INFO] DFAST Taxonomy check result was written to GCF_018141445.1_ASM1814144v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:59,803] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:59,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:59,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/checkm_data
[2024-01-24 10:47:59,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:59,877] [INFO] Task started: CheckM
[2024-01-24 10:47:59,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018141445.1_ASM1814144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018141445.1_ASM1814144v1_genomic.fna/checkm_input GCF_018141445.1_ASM1814144v1_genomic.fna/checkm_result
[2024-01-24 10:48:47,067] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:47,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:47,094] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:47,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:47,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018141445.1_ASM1814144v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:47,095] [INFO] Task started: Blastn
[2024-01-24 10:48:47,095] [INFO] Running command: blastn -query GCF_018141445.1_ASM1814144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71e90332-1142-4333-84c9-dbc6fa26d5bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_018141445.1_ASM1814144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:48,141] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:48,146] [INFO] Selected 29 target genomes.
[2024-01-24 10:48:48,147] [INFO] Target genome list was writen to GCF_018141445.1_ASM1814144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:48,168] [INFO] Task started: fastANI
[2024-01-24 10:48:48,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgf81bf4da-39d5-4090-8f2e-d3fdc5e366fb/GCF_018141445.1_ASM1814144v1_genomic.fna.gz --refList GCF_018141445.1_ASM1814144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018141445.1_ASM1814144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:05,004] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:05,009] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:05,010] [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_018141445.1	s__Vallitalea pronyensis	100.0	2108	2108	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018141425.1	s__Vallitalea guaymasensis	78.2013	282	2108	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	97.34	97.34	0.88	0.88	2	-
GCF_004339095.1	s__Natranaerovirga hydrolytica	76.6198	56	2108	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__DSM-24629;g__Natranaerovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:05,011] [INFO] GTDB search result was written to GCF_018141445.1_ASM1814144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:05,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:05,015] [INFO] DFAST_QC result json was written to GCF_018141445.1_ASM1814144v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:05,016] [INFO] DFAST_QC completed!
[2024-01-24 10:49:05,016] [INFO] Total running time: 0h1m53s